diff --git a/runatlantis.io/docs/automerging.md b/runatlantis.io/docs/automerging.md
index 2716a572ee..d1438eec54 100644
--- a/runatlantis.io/docs/automerging.md
+++ b/runatlantis.io/docs/automerging.md
@@ -29,6 +29,20 @@ Automerging can be enabled either by:
 If automerge is enabled, you can disable it for a single `atlantis apply`
 command with the `--auto-merge-disabled` option.
 
+## How to set merge method for automerge
+
+If automerge is enabled, you can use `--merge-method` option
+for `atlantis apply` command to specify which merge method use.
+
+```shell
+atlantis apply --merge-method squash
+```
+
+Implemented only for GitHub. You can choose one of them:
+- merge
+- rebase
+- squash
+
 ## Requirements
 
 ### All Plans Must Succeed
diff --git a/runatlantis.io/docs/using-atlantis.md b/runatlantis.io/docs/using-atlantis.md
index 61c06e1a21..2b4b941dcd 100644
--- a/runatlantis.io/docs/using-atlantis.md
+++ b/runatlantis.io/docs/using-atlantis.md
@@ -149,6 +149,7 @@ atlantis apply -w staging
 * `-p project` Apply the plan for this project. Refers to the name of the project configured in the repo's [`atlantis.yaml` file](repo-level-atlantis-yaml.md). Cannot be used at same time as `-d` or `-w`.
 * `-w workspace` Apply the plan for this [Terraform workspace](https://developer.hashicorp.com/terraform/language/state/workspaces). Ignore this if Terraform workspaces are unused.
 * `--auto-merge-disabled` Disable [automerge](automerging.md) for this apply command.
+* `--merge-method method` Specify which [merge method](automerging.md#how-to-set-merge-method-for-automerge) use for apply command if [automerge](automerging.md) is enabled. Implemented only for GitHub.
 * `--verbose` Append Atlantis log to comment.
 
 ### Additional Terraform flags
diff --git a/server/core/config/valid/global_cfg.go b/server/core/config/valid/global_cfg.go
index 11a267c151..cb1c9e0f3e 100644
--- a/server/core/config/valid/global_cfg.go
+++ b/server/core/config/valid/global_cfg.go
@@ -104,6 +104,7 @@ type MergedProjectCfg struct {
 	Name                      string
 	AutoplanEnabled           bool
 	AutoMergeDisabled         bool
+	MergeMethod               string
 	TerraformVersion          *version.Version
 	RepoCfgVersion            int
 	PolicySets                PolicySets
diff --git a/server/events/apply_command_runner.go b/server/events/apply_command_runner.go
index ee6bf8ab1f..3f4340b99a 100644
--- a/server/events/apply_command_runner.go
+++ b/server/events/apply_command_runner.go
@@ -181,7 +181,7 @@ func (a *ApplyCommandRunner) Run(ctx *command.Context, cmd *CommentCommand) {
 	a.updateCommitStatus(ctx, pullStatus)
 
 	if a.autoMerger.automergeEnabled(projectCmds) && !cmd.AutoMergeDisabled {
-		a.autoMerger.automerge(ctx, pullStatus, a.autoMerger.deleteSourceBranchOnMergeEnabled(projectCmds))
+		a.autoMerger.automerge(ctx, pullStatus, a.autoMerger.deleteSourceBranchOnMergeEnabled(projectCmds), cmd.MergeMethod)
 	}
 }
 
diff --git a/server/events/automerger.go b/server/events/automerger.go
index fa74beac0f..1d19964076 100644
--- a/server/events/automerger.go
+++ b/server/events/automerger.go
@@ -13,7 +13,7 @@ type AutoMerger struct {
 	GlobalAutomerge bool
 }
 
-func (c *AutoMerger) automerge(ctx *command.Context, pullStatus models.PullStatus, deleteSourceBranchOnMerge bool) {
+func (c *AutoMerger) automerge(ctx *command.Context, pullStatus models.PullStatus, deleteSourceBranchOnMerge bool, mergeMethod string) {
 	// We only automerge if all projects have been successfully applied.
 	for _, p := range pullStatus.Projects {
 		if p.Status != models.AppliedPlanStatus {
@@ -32,6 +32,7 @@ func (c *AutoMerger) automerge(ctx *command.Context, pullStatus models.PullStatu
 	ctx.Log.Info("automerging pull request")
 	var pullOptions models.PullRequestOptions
 	pullOptions.DeleteSourceBranchOnMerge = deleteSourceBranchOnMerge
+	pullOptions.MergeMethod = mergeMethod
 	err := c.VCSClient.MergePull(ctx.Log, ctx.Pull, pullOptions)
 
 	if err != nil {
diff --git a/server/events/comment_parser.go b/server/events/comment_parser.go
index 3b3d2d3b0a..5a14f8a838 100644
--- a/server/events/comment_parser.go
+++ b/server/events/comment_parser.go
@@ -41,6 +41,8 @@ const (
 	policySetFlagShort           = ""
 	autoMergeDisabledFlagLong    = "auto-merge-disabled"
 	autoMergeDisabledFlagShort   = ""
+	mergeMethodFlagLong          = "merge-method"
+	mergeMethodFlagShort         = ""
 	verboseFlagLong              = "verbose"
 	verboseFlagShort             = ""
 	clearPolicyApprovalFlagLong  = "clear-policy-approval"
@@ -70,7 +72,7 @@ type CommentBuilder interface {
 	// BuildPlanComment builds a plan comment for the specified args.
 	BuildPlanComment(repoRelDir string, workspace string, project string, commentArgs []string) string
 	// BuildApplyComment builds an apply comment for the specified args.
-	BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool) string
+	BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool, mergeMethod string) string
 	// BuildApprovePoliciesComment builds an approve_policies comment for the specified args.
 	BuildApprovePoliciesComment(repoRelDir string, workspace string, project string) string
 }
@@ -226,7 +228,9 @@ func (e *CommentParser) Parse(rawComment string, vcsHost models.VCSHostType) Com
 	var project string
 	var policySet string
 	var clearPolicyApproval bool
-	var verbose, autoMergeDisabled bool
+	var verbose bool
+	var autoMergeDisabled bool
+	var mergeMethod string
 	var flagSet *pflag.FlagSet
 	var name command.Name
 
@@ -248,6 +252,7 @@ func (e *CommentParser) Parse(rawComment string, vcsHost models.VCSHostType) Com
 		flagSet.StringVarP(&dir, dirFlagLong, dirFlagShort, "", "Apply the plan for this directory, relative to root of repo, ex. 'child/dir'.")
 		flagSet.StringVarP(&project, projectFlagLong, projectFlagShort, "", "Apply the plan for this project. Refers to the name of the project configured in a repo config file. Cannot be used at same time as workspace or dir flags.")
 		flagSet.BoolVarP(&autoMergeDisabled, autoMergeDisabledFlagLong, autoMergeDisabledFlagShort, false, "Disable automerge after apply.")
+		flagSet.StringVarP(&mergeMethod, mergeMethodFlagLong, mergeMethodFlagShort, "", "Specifies merge method for the VCS if automerge is enabled.")
 		flagSet.BoolVarP(&verbose, verboseFlagLong, verboseFlagShort, false, "Append Atlantis log to comment.")
 	case command.ApprovePolicies.String():
 		name = command.ApprovePolicies
@@ -317,8 +322,20 @@ func (e *CommentParser) Parse(rawComment string, vcsHost models.VCSHostType) Com
 		return CommentParseResult{CommentResponse: e.errMarkdown(err, cmd, flagSet)}
 	}
 
+	if mergeMethod != "" {
+		if autoMergeDisabled {
+			err := fmt.Sprintf("cannot use --%s at same time with --%s", mergeMethodFlagLong, autoMergeDisabledFlagLong)
+			return CommentParseResult{CommentResponse: e.errMarkdown(err, cmd, flagSet)}
+		}
+
+		if vcsHost != models.Github {
+			err := fmt.Sprintf("--%s not implemeted for %s", mergeMethodFlagLong, vcsHost.String())
+			return CommentParseResult{CommentResponse: e.errMarkdown(err, cmd, flagSet)}
+		}
+	}
+
 	return CommentParseResult{
-		Command: NewCommentCommand(dir, extraArgs, name, subName, verbose, autoMergeDisabled, workspace, project, policySet, clearPolicyApproval),
+		Command: NewCommentCommand(dir, extraArgs, name, subName, verbose, autoMergeDisabled, mergeMethod, workspace, project, policySet, clearPolicyApproval),
 	}
 }
 
@@ -387,7 +404,7 @@ func (e *CommentParser) parseArgs(name command.Name, args []string, flagSet *pfl
 
 // BuildPlanComment builds a plan comment for the specified args.
 func (e *CommentParser) BuildPlanComment(repoRelDir string, workspace string, project string, commentArgs []string) string {
-	flags := e.buildFlags(repoRelDir, workspace, project, false)
+	flags := e.buildFlags(repoRelDir, workspace, project, false, "")
 	commentFlags := ""
 	if len(commentArgs) > 0 {
 		var flagsWithoutQuotes []string
@@ -402,18 +419,18 @@ func (e *CommentParser) BuildPlanComment(repoRelDir string, workspace string, pr
 }
 
 // BuildApplyComment builds an apply comment for the specified args.
-func (e *CommentParser) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool) string {
-	flags := e.buildFlags(repoRelDir, workspace, project, autoMergeDisabled)
+func (e *CommentParser) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool, mergeMethod string) string {
+	flags := e.buildFlags(repoRelDir, workspace, project, autoMergeDisabled, mergeMethod)
 	return fmt.Sprintf("%s %s%s", e.ExecutableName, command.Apply.String(), flags)
 }
 
 // BuildApprovePoliciesComment builds an apply comment for the specified args.
 func (e *CommentParser) BuildApprovePoliciesComment(repoRelDir string, workspace string, project string) string {
-	flags := e.buildFlags(repoRelDir, workspace, project, false)
+	flags := e.buildFlags(repoRelDir, workspace, project, false, "")
 	return fmt.Sprintf("%s %s%s", e.ExecutableName, command.ApprovePolicies.String(), flags)
 }
 
-func (e *CommentParser) buildFlags(repoRelDir string, workspace string, project string, autoMergeDisabled bool) string {
+func (e *CommentParser) buildFlags(repoRelDir string, workspace string, project string, autoMergeDisabled bool, mergeMethod string) string {
 	// Add quotes if dir has spaces.
 	if strings.Contains(repoRelDir, " ") {
 		repoRelDir = fmt.Sprintf("%q", repoRelDir)
@@ -441,6 +458,9 @@ func (e *CommentParser) buildFlags(repoRelDir string, workspace string, project
 	if autoMergeDisabled {
 		flags = fmt.Sprintf("%s --%s", flags, autoMergeDisabledFlagLong)
 	}
+	if mergeMethod != "" {
+		flags = fmt.Sprintf("%s --%s %s", flags, mergeMethodFlagLong, mergeMethod)
+	}
 	return flags
 }
 
diff --git a/server/events/comment_parser_test.go b/server/events/comment_parser_test.go
index 45c22e7e5f..05c0e9db64 100644
--- a/server/events/comment_parser_test.go
+++ b/server/events/comment_parser_test.go
@@ -729,6 +729,7 @@ func TestBuildPlanApplyVersionComment(t *testing.T) {
 		workspace         string
 		project           string
 		autoMergeDisabled bool
+		mergeMethod       string
 		commentArgs       []string
 		expPlanFlags      string
 		expApplyFlags     string
@@ -824,6 +825,16 @@ func TestBuildPlanApplyVersionComment(t *testing.T) {
 			expApplyFlags:     "-d dir -w workspace --auto-merge-disabled",
 			expVersionFlags:   "-d dir -w workspace",
 		},
+		{
+			repoRelDir:      "dir",
+			workspace:       "workspace",
+			project:         "",
+			mergeMethod:     "squash",
+			commentArgs:     []string{`"arg1"`, `"arg2"`, `arg3`},
+			expPlanFlags:    "-d dir -w workspace -- arg1 arg2 arg3",
+			expApplyFlags:   "-d dir -w workspace --merge-method squash",
+			expVersionFlags: "-d dir -w workspace",
+		},
 	}
 
 	for _, c := range cases {
@@ -834,7 +845,7 @@ func TestBuildPlanApplyVersionComment(t *testing.T) {
 					actComment := commentParser.BuildPlanComment(c.repoRelDir, c.workspace, c.project, c.commentArgs)
 					Equals(t, fmt.Sprintf("atlantis plan %s", c.expPlanFlags), actComment)
 				case command.Apply:
-					actComment := commentParser.BuildApplyComment(c.repoRelDir, c.workspace, c.project, c.autoMergeDisabled)
+					actComment := commentParser.BuildApplyComment(c.repoRelDir, c.workspace, c.project, c.autoMergeDisabled, c.mergeMethod)
 					Equals(t, fmt.Sprintf("atlantis apply %s", c.expApplyFlags), actComment)
 				}
 			}
@@ -1023,6 +1034,7 @@ var ApplyUsage = `Usage of apply:
       --auto-merge-disabled   Disable automerge after apply.
   -d, --dir string            Apply the plan for this directory, relative to root of
                               repo, ex. 'child/dir'.
+      --merge-method string   Specifies merge method for the VCS if automerge is enabled.
   -p, --project string        Apply the plan for this project. Refers to the name of
                               the project configured in a repo config file. Cannot
                               be used at same time as workspace or dir flags.
diff --git a/server/events/event_parser.go b/server/events/event_parser.go
index e2283d4d3a..9b1c0673a1 100644
--- a/server/events/event_parser.go
+++ b/server/events/event_parser.go
@@ -128,6 +128,8 @@ type CommentCommand struct {
 	SubName string
 	// AutoMergeDisabled is true if the command should not automerge after apply.
 	AutoMergeDisabled bool
+	// MergeMethod specified the merge method for the VCS if automerge enabled.
+	MergeMethod string
 	// Verbose is true if the command should output verbosely.
 	Verbose bool
 	// Workspace is the name of the Terraform workspace to run the command in.
@@ -177,11 +179,11 @@ func (c CommentCommand) IsAutoplan() bool {
 
 // String returns a string representation of the command.
 func (c CommentCommand) String() string {
-	return fmt.Sprintf("command=%q verbose=%t dir=%q workspace=%q project=%q policyset=%q, clear-policy-approval=%t, flags=%q", c.Name.String(), c.Verbose, c.RepoRelDir, c.Workspace, c.ProjectName, c.PolicySet, c.ClearPolicyApproval, strings.Join(c.Flags, ","))
+	return fmt.Sprintf("command=%q, verbose=%t, dir=%q, workspace=%q, project=%q, policyset=%q, auto-merge-disabled=%t, merge-method=%s, clear-policy-approval=%t, flags=%q", c.Name.String(), c.Verbose, c.RepoRelDir, c.Workspace, c.ProjectName, c.PolicySet, c.AutoMergeDisabled, c.MergeMethod, c.ClearPolicyApproval, strings.Join(c.Flags, ","))
 }
 
 // NewCommentCommand constructs a CommentCommand, setting all missing fields to defaults.
-func NewCommentCommand(repoRelDir string, flags []string, name command.Name, subName string, verbose, autoMergeDisabled bool, workspace string, project string, policySet string, clearPolicyApproval bool) *CommentCommand {
+func NewCommentCommand(repoRelDir string, flags []string, name command.Name, subName string, verbose, autoMergeDisabled bool, mergeMethod string, workspace string, project string, policySet string, clearPolicyApproval bool) *CommentCommand {
 	// If repoRelDir was empty we want to keep it that way to indicate that it
 	// wasn't specified in the comment.
 	if repoRelDir != "" {
@@ -198,6 +200,7 @@ func NewCommentCommand(repoRelDir string, flags []string, name command.Name, sub
 		Verbose:             verbose,
 		Workspace:           workspace,
 		AutoMergeDisabled:   autoMergeDisabled,
+		MergeMethod:         mergeMethod,
 		ProjectName:         project,
 		PolicySet:           policySet,
 		ClearPolicyApproval: clearPolicyApproval,
diff --git a/server/events/event_parser_test.go b/server/events/event_parser_test.go
index a136a3ab8b..87596afe81 100644
--- a/server/events/event_parser_test.go
+++ b/server/events/event_parser_test.go
@@ -750,14 +750,14 @@ func TestNewCommand_CleansDir(t *testing.T) {
 
 	for _, c := range cases {
 		t.Run(c.RepoRelDir, func(t *testing.T) {
-			cmd := events.NewCommentCommand(c.RepoRelDir, nil, command.Plan, "", false, false, "workspace", "", "", false)
+			cmd := events.NewCommentCommand(c.RepoRelDir, nil, command.Plan, "", false, false, "", "workspace", "", "", false)
 			Equals(t, c.ExpDir, cmd.RepoRelDir)
 		})
 	}
 }
 
 func TestNewCommand_EmptyDirWorkspaceProject(t *testing.T) {
-	cmd := events.NewCommentCommand("", nil, command.Plan, "", false, false, "", "", "", false)
+	cmd := events.NewCommentCommand("", nil, command.Plan, "", false, false, "", "", "", "", false)
 	Equals(t, events.CommentCommand{
 		RepoRelDir:  "",
 		Flags:       nil,
@@ -769,7 +769,7 @@ func TestNewCommand_EmptyDirWorkspaceProject(t *testing.T) {
 }
 
 func TestNewCommand_AllFieldsSet(t *testing.T) {
-	cmd := events.NewCommentCommand("dir", []string{"a", "b"}, command.Plan, "", true, false, "workspace", "project", "policyset", false)
+	cmd := events.NewCommentCommand("dir", []string{"a", "b"}, command.Plan, "", true, false, "", "workspace", "project", "policyset", false)
 	Equals(t, events.CommentCommand{
 		Workspace:   "workspace",
 		RepoRelDir:  "dir",
@@ -816,7 +816,7 @@ func TestCommentCommand_IsAutoplan(t *testing.T) {
 }
 
 func TestCommentCommand_String(t *testing.T) {
-	exp := `command="plan" verbose=true dir="mydir" workspace="myworkspace" project="myproject" policyset="", clear-policy-approval=false, flags="flag1,flag2"`
+	exp := `command="plan", verbose=true, dir="mydir", workspace="myworkspace", project="myproject", policyset="", auto-merge-disabled=false, merge-method=, clear-policy-approval=false, flags="flag1,flag2"`
 	Equals(t, exp, (events.CommentCommand{
 		RepoRelDir:  "mydir",
 		Flags:       []string{"flag1", "flag2"},
diff --git a/server/events/mocks/mock_comment_building.go b/server/events/mocks/mock_comment_building.go
index 1e461a07ee..1d25d4eacd 100644
--- a/server/events/mocks/mock_comment_building.go
+++ b/server/events/mocks/mock_comment_building.go
@@ -24,49 +24,49 @@ func NewMockCommentBuilder(options ...pegomock.Option) *MockCommentBuilder {
 func (mock *MockCommentBuilder) SetFailHandler(fh pegomock.FailHandler) { mock.fail = fh }
 func (mock *MockCommentBuilder) FailHandler() pegomock.FailHandler      { return mock.fail }
 
-func (mock *MockCommentBuilder) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool) string {
+func (mock *MockCommentBuilder) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool, mergeMethod string) string {
 	if mock == nil {
 		panic("mock must not be nil. Use myMock := NewMockCommentBuilder().")
 	}
-	params := []pegomock.Param{repoRelDir, workspace, project, autoMergeDisabled}
-	result := pegomock.GetGenericMockFrom(mock).Invoke("BuildApplyComment", params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
-	var ret0 string
-	if len(result) != 0 {
-		if result[0] != nil {
-			ret0 = result[0].(string)
+	_params := []pegomock.Param{repoRelDir, workspace, project, autoMergeDisabled, mergeMethod}
+	_result := pegomock.GetGenericMockFrom(mock).Invoke("BuildApplyComment", _params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
+	var _ret0 string
+	if len(_result) != 0 {
+		if _result[0] != nil {
+			_ret0 = _result[0].(string)
 		}
 	}
-	return ret0
+	return _ret0
 }
 
 func (mock *MockCommentBuilder) BuildApprovePoliciesComment(repoRelDir string, workspace string, project string) string {
 	if mock == nil {
 		panic("mock must not be nil. Use myMock := NewMockCommentBuilder().")
 	}
-	params := []pegomock.Param{repoRelDir, workspace, project}
-	result := pegomock.GetGenericMockFrom(mock).Invoke("BuildApprovePoliciesComment", params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
-	var ret0 string
-	if len(result) != 0 {
-		if result[0] != nil {
-			ret0 = result[0].(string)
+	_params := []pegomock.Param{repoRelDir, workspace, project}
+	_result := pegomock.GetGenericMockFrom(mock).Invoke("BuildApprovePoliciesComment", _params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
+	var _ret0 string
+	if len(_result) != 0 {
+		if _result[0] != nil {
+			_ret0 = _result[0].(string)
 		}
 	}
-	return ret0
+	return _ret0
 }
 
 func (mock *MockCommentBuilder) BuildPlanComment(repoRelDir string, workspace string, project string, commentArgs []string) string {
 	if mock == nil {
 		panic("mock must not be nil. Use myMock := NewMockCommentBuilder().")
 	}
-	params := []pegomock.Param{repoRelDir, workspace, project, commentArgs}
-	result := pegomock.GetGenericMockFrom(mock).Invoke("BuildPlanComment", params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
-	var ret0 string
-	if len(result) != 0 {
-		if result[0] != nil {
-			ret0 = result[0].(string)
+	_params := []pegomock.Param{repoRelDir, workspace, project, commentArgs}
+	_result := pegomock.GetGenericMockFrom(mock).Invoke("BuildPlanComment", _params, []reflect.Type{reflect.TypeOf((*string)(nil)).Elem()})
+	var _ret0 string
+	if len(_result) != 0 {
+		if _result[0] != nil {
+			_ret0 = _result[0].(string)
 		}
 	}
-	return ret0
+	return _ret0
 }
 
 func (mock *MockCommentBuilder) VerifyWasCalledOnce() *VerifierMockCommentBuilder {
@@ -106,9 +106,9 @@ type VerifierMockCommentBuilder struct {
 	timeout                time.Duration
 }
 
-func (verifier *VerifierMockCommentBuilder) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool) *MockCommentBuilder_BuildApplyComment_OngoingVerification {
-	params := []pegomock.Param{repoRelDir, workspace, project, autoMergeDisabled}
-	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildApplyComment", params, verifier.timeout)
+func (verifier *VerifierMockCommentBuilder) BuildApplyComment(repoRelDir string, workspace string, project string, autoMergeDisabled bool, mergeMethod string) *MockCommentBuilder_BuildApplyComment_OngoingVerification {
+	_params := []pegomock.Param{repoRelDir, workspace, project, autoMergeDisabled, mergeMethod}
+	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildApplyComment", _params, verifier.timeout)
 	return &MockCommentBuilder_BuildApplyComment_OngoingVerification{mock: verifier.mock, methodInvocations: methodInvocations}
 }
 
@@ -117,37 +117,51 @@ type MockCommentBuilder_BuildApplyComment_OngoingVerification struct {
 	methodInvocations []pegomock.MethodInvocation
 }
 
-func (c *MockCommentBuilder_BuildApplyComment_OngoingVerification) GetCapturedArguments() (string, string, string, bool) {
-	repoRelDir, workspace, project, autoMergeDisabled := c.GetAllCapturedArguments()
-	return repoRelDir[len(repoRelDir)-1], workspace[len(workspace)-1], project[len(project)-1], autoMergeDisabled[len(autoMergeDisabled)-1]
+func (c *MockCommentBuilder_BuildApplyComment_OngoingVerification) GetCapturedArguments() (string, string, string, bool, string) {
+	repoRelDir, workspace, project, autoMergeDisabled, mergeMethod := c.GetAllCapturedArguments()
+	return repoRelDir[len(repoRelDir)-1], workspace[len(workspace)-1], project[len(project)-1], autoMergeDisabled[len(autoMergeDisabled)-1], mergeMethod[len(mergeMethod)-1]
 }
 
-func (c *MockCommentBuilder_BuildApplyComment_OngoingVerification) GetAllCapturedArguments() (_param0 []string, _param1 []string, _param2 []string, _param3 []bool) {
-	params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
-	if len(params) > 0 {
-		_param0 = make([]string, len(c.methodInvocations))
-		for u, param := range params[0] {
-			_param0[u] = param.(string)
+func (c *MockCommentBuilder_BuildApplyComment_OngoingVerification) GetAllCapturedArguments() (_param0 []string, _param1 []string, _param2 []string, _param3 []bool, _param4 []string) {
+	_params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
+	if len(_params) > 0 {
+		if len(_params) > 0 {
+			_param0 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[0] {
+				_param0[u] = param.(string)
+			}
 		}
-		_param1 = make([]string, len(c.methodInvocations))
-		for u, param := range params[1] {
-			_param1[u] = param.(string)
+		if len(_params) > 1 {
+			_param1 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[1] {
+				_param1[u] = param.(string)
+			}
 		}
-		_param2 = make([]string, len(c.methodInvocations))
-		for u, param := range params[2] {
-			_param2[u] = param.(string)
+		if len(_params) > 2 {
+			_param2 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[2] {
+				_param2[u] = param.(string)
+			}
 		}
-		_param3 = make([]bool, len(c.methodInvocations))
-		for u, param := range params[3] {
-			_param3[u] = param.(bool)
+		if len(_params) > 3 {
+			_param3 = make([]bool, len(c.methodInvocations))
+			for u, param := range _params[3] {
+				_param3[u] = param.(bool)
+			}
+		}
+		if len(_params) > 4 {
+			_param4 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[4] {
+				_param4[u] = param.(string)
+			}
 		}
 	}
 	return
 }
 
 func (verifier *VerifierMockCommentBuilder) BuildApprovePoliciesComment(repoRelDir string, workspace string, project string) *MockCommentBuilder_BuildApprovePoliciesComment_OngoingVerification {
-	params := []pegomock.Param{repoRelDir, workspace, project}
-	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildApprovePoliciesComment", params, verifier.timeout)
+	_params := []pegomock.Param{repoRelDir, workspace, project}
+	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildApprovePoliciesComment", _params, verifier.timeout)
 	return &MockCommentBuilder_BuildApprovePoliciesComment_OngoingVerification{mock: verifier.mock, methodInvocations: methodInvocations}
 }
 
@@ -162,27 +176,33 @@ func (c *MockCommentBuilder_BuildApprovePoliciesComment_OngoingVerification) Get
 }
 
 func (c *MockCommentBuilder_BuildApprovePoliciesComment_OngoingVerification) GetAllCapturedArguments() (_param0 []string, _param1 []string, _param2 []string) {
-	params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
-	if len(params) > 0 {
-		_param0 = make([]string, len(c.methodInvocations))
-		for u, param := range params[0] {
-			_param0[u] = param.(string)
+	_params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
+	if len(_params) > 0 {
+		if len(_params) > 0 {
+			_param0 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[0] {
+				_param0[u] = param.(string)
+			}
 		}
-		_param1 = make([]string, len(c.methodInvocations))
-		for u, param := range params[1] {
-			_param1[u] = param.(string)
+		if len(_params) > 1 {
+			_param1 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[1] {
+				_param1[u] = param.(string)
+			}
 		}
-		_param2 = make([]string, len(c.methodInvocations))
-		for u, param := range params[2] {
-			_param2[u] = param.(string)
+		if len(_params) > 2 {
+			_param2 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[2] {
+				_param2[u] = param.(string)
+			}
 		}
 	}
 	return
 }
 
 func (verifier *VerifierMockCommentBuilder) BuildPlanComment(repoRelDir string, workspace string, project string, commentArgs []string) *MockCommentBuilder_BuildPlanComment_OngoingVerification {
-	params := []pegomock.Param{repoRelDir, workspace, project, commentArgs}
-	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildPlanComment", params, verifier.timeout)
+	_params := []pegomock.Param{repoRelDir, workspace, project, commentArgs}
+	methodInvocations := pegomock.GetGenericMockFrom(verifier.mock).Verify(verifier.inOrderContext, verifier.invocationCountMatcher, "BuildPlanComment", _params, verifier.timeout)
 	return &MockCommentBuilder_BuildPlanComment_OngoingVerification{mock: verifier.mock, methodInvocations: methodInvocations}
 }
 
@@ -197,23 +217,31 @@ func (c *MockCommentBuilder_BuildPlanComment_OngoingVerification) GetCapturedArg
 }
 
 func (c *MockCommentBuilder_BuildPlanComment_OngoingVerification) GetAllCapturedArguments() (_param0 []string, _param1 []string, _param2 []string, _param3 [][]string) {
-	params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
-	if len(params) > 0 {
-		_param0 = make([]string, len(c.methodInvocations))
-		for u, param := range params[0] {
-			_param0[u] = param.(string)
+	_params := pegomock.GetGenericMockFrom(c.mock).GetInvocationParams(c.methodInvocations)
+	if len(_params) > 0 {
+		if len(_params) > 0 {
+			_param0 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[0] {
+				_param0[u] = param.(string)
+			}
 		}
-		_param1 = make([]string, len(c.methodInvocations))
-		for u, param := range params[1] {
-			_param1[u] = param.(string)
+		if len(_params) > 1 {
+			_param1 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[1] {
+				_param1[u] = param.(string)
+			}
 		}
-		_param2 = make([]string, len(c.methodInvocations))
-		for u, param := range params[2] {
-			_param2[u] = param.(string)
+		if len(_params) > 2 {
+			_param2 = make([]string, len(c.methodInvocations))
+			for u, param := range _params[2] {
+				_param2[u] = param.(string)
+			}
 		}
-		_param3 = make([][]string, len(c.methodInvocations))
-		for u, param := range params[3] {
-			_param3[u] = param.([]string)
+		if len(_params) > 3 {
+			_param3 = make([][]string, len(c.methodInvocations))
+			for u, param := range _params[3] {
+				_param3[u] = param.([]string)
+			}
 		}
 	}
 	return
diff --git a/server/events/models/models.go b/server/events/models/models.go
index fe5c0ee09d..f7bd4790db 100644
--- a/server/events/models/models.go
+++ b/server/events/models/models.go
@@ -185,6 +185,9 @@ type PullRequestOptions struct {
 	// When DeleteSourceBranchOnMerge flag is set to true VCS deletes the source branch after the PR is merged
 	// Applied by GitLab & AzureDevops
 	DeleteSourceBranchOnMerge bool
+	// MergeMethod specifies the merge method for the VCS
+	// Implemented only for Github
+	MergeMethod string
 }
 
 type PullRequestState int
diff --git a/server/events/project_command_context_builder.go b/server/events/project_command_context_builder.go
index 05d61fda6d..7989c32466 100644
--- a/server/events/project_command_context_builder.go
+++ b/server/events/project_command_context_builder.go
@@ -130,7 +130,7 @@ func (cb *DefaultProjectCommandContextBuilder) BuildProjectContext(
 	projectCmdContext := newProjectCommandContext(
 		ctx,
 		cmdName,
-		cb.CommentBuilder.BuildApplyComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, prjCfg.AutoMergeDisabled),
+		cb.CommentBuilder.BuildApplyComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, prjCfg.AutoMergeDisabled, prjCfg.MergeMethod),
 		cb.CommentBuilder.BuildApprovePoliciesComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name),
 		cb.CommentBuilder.BuildPlanComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, commentFlags),
 		prjCfg,
@@ -203,7 +203,7 @@ func (cb *PolicyCheckProjectCommandContextBuilder) BuildProjectContext(
 		projectCmds = append(projectCmds, newProjectCommandContext(
 			ctx,
 			command.PolicyCheck,
-			cb.CommentBuilder.BuildApplyComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, prjCfg.AutoMergeDisabled),
+			cb.CommentBuilder.BuildApplyComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, prjCfg.AutoMergeDisabled, prjCfg.MergeMethod),
 			cb.CommentBuilder.BuildApprovePoliciesComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name),
 			cb.CommentBuilder.BuildPlanComment(prjCfg.RepoRelDir, prjCfg.Workspace, prjCfg.Name, commentFlags),
 			prjCfg,
diff --git a/server/events/project_command_context_builder_test.go b/server/events/project_command_context_builder_test.go
index c3d75e950c..84ce0ff630 100644
--- a/server/events/project_command_context_builder_test.go
+++ b/server/events/project_command_context_builder_test.go
@@ -51,7 +51,7 @@ func TestProjectCommandContextBuilder_PullStatus(t *testing.T) {
 
 	t.Run("with project name defined", func(t *testing.T) {
 		When(mockCommentBuilder.BuildPlanComment(projRepoRelDir, projWorkspace, projName, []string{})).ThenReturn(expectedPlanCmt)
-		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, projName, false)).ThenReturn(expectedApplyCmt)
+		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, projName, false, "")).ThenReturn(expectedApplyCmt)
 
 		pullStatus.Projects = []models.ProjectStatus{
 			{
@@ -68,7 +68,7 @@ func TestProjectCommandContextBuilder_PullStatus(t *testing.T) {
 	t.Run("with no project name defined", func(t *testing.T) {
 		projCfg.Name = ""
 		When(mockCommentBuilder.BuildPlanComment(projRepoRelDir, projWorkspace, "", []string{})).ThenReturn(expectedPlanCmt)
-		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false)).ThenReturn(expectedApplyCmt)
+		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false, "")).ThenReturn(expectedApplyCmt)
 		pullStatus.Projects = []models.ProjectStatus{
 			{
 				Status:     models.ErroredPlanStatus,
@@ -88,7 +88,7 @@ func TestProjectCommandContextBuilder_PullStatus(t *testing.T) {
 	t.Run("when ParallelApply is set to true", func(t *testing.T) {
 		projCfg.Name = "Apply Comment"
 		When(mockCommentBuilder.BuildPlanComment(projRepoRelDir, projWorkspace, "", []string{})).ThenReturn(expectedPlanCmt)
-		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false)).ThenReturn(expectedApplyCmt)
+		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false, "")).ThenReturn(expectedApplyCmt)
 		pullStatus.Projects = []models.ProjectStatus{
 			{
 				Status:     models.ErroredPlanStatus,
@@ -109,7 +109,7 @@ func TestProjectCommandContextBuilder_PullStatus(t *testing.T) {
 	t.Run("when AbortOnExcecutionOrderFail is set to true", func(t *testing.T) {
 		projCfg.Name = "Apply Comment"
 		When(mockCommentBuilder.BuildPlanComment(projRepoRelDir, projWorkspace, "", []string{})).ThenReturn(expectedPlanCmt)
-		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false)).ThenReturn(expectedApplyCmt)
+		When(mockCommentBuilder.BuildApplyComment(projRepoRelDir, projWorkspace, "", false, "")).ThenReturn(expectedApplyCmt)
 		pullStatus.Projects = []models.ProjectStatus{
 			{
 				Status:     models.ErroredPlanStatus,
diff --git a/server/events/vcs/github_client.go b/server/events/vcs/github_client.go
index 1129867064..2b5ca4085c 100644
--- a/server/events/vcs/github_client.go
+++ b/server/events/vcs/github_client.go
@@ -17,7 +17,9 @@ import (
 	"context"
 	"encoding/base64"
 	"fmt"
+	"maps"
 	"net/http"
+	"slices"
 	"strconv"
 	"strings"
 	"time"
@@ -884,7 +886,7 @@ func (g *GithubClient) UpdateStatus(logger logging.SimpleLogging, repo models.Re
 }
 
 // MergePull merges the pull request.
-func (g *GithubClient) MergePull(logger logging.SimpleLogging, pull models.PullRequest, _ models.PullRequestOptions) error {
+func (g *GithubClient) MergePull(logger logging.SimpleLogging, pull models.PullRequest, pullOptions models.PullRequestOptions) error {
 	logger.Debug("Merging GitHub pull request %d", pull.Num)
 	// Users can set their repo to disallow certain types of merging.
 	// We detect which types aren't allowed and use the type that is.
@@ -895,17 +897,39 @@ func (g *GithubClient) MergePull(logger logging.SimpleLogging, pull models.PullR
 	if err != nil {
 		return errors.Wrap(err, "fetching repo info")
 	}
+
 	const (
 		defaultMergeMethod = "merge"
 		rebaseMergeMethod  = "rebase"
 		squashMergeMethod  = "squash"
 	)
-	method := defaultMergeMethod
-	if !repo.GetAllowMergeCommit() {
-		if repo.GetAllowRebaseMerge() {
-			method = rebaseMergeMethod
-		} else if repo.GetAllowSquashMerge() {
-			method = squashMergeMethod
+
+	mergeMethods := map[string]func() bool{
+		defaultMergeMethod: repo.GetAllowMergeCommit,
+		rebaseMergeMethod:  repo.GetAllowRebaseMerge,
+		squashMergeMethod:  repo.GetAllowSquashMerge,
+	}
+
+	var method string
+	if pullOptions.MergeMethod != "" {
+		method = pullOptions.MergeMethod
+
+		isMethodAllowed, isMethodExist := mergeMethods[method]
+		if !isMethodExist {
+			return fmt.Errorf("%s method is unknown for GitHub, use one of them: %v", method, slices.Collect(maps.Keys(mergeMethods)))
+		}
+
+		if !isMethodAllowed() {
+			return fmt.Errorf("%s method is not allowed by repository settings", method)
+		}
+	} else {
+		method = defaultMergeMethod
+		if !repo.GetAllowMergeCommit() {
+			if repo.GetAllowRebaseMerge() {
+				method = rebaseMergeMethod
+			} else if repo.GetAllowSquashMerge() {
+				method = squashMergeMethod
+			}
 		}
 	}
 
diff --git a/server/events/vcs/github_client_test.go b/server/events/vcs/github_client_test.go
index ef97c64245..bbe0ffbea3 100644
--- a/server/events/vcs/github_client_test.go
+++ b/server/events/vcs/github_client_test.go
@@ -977,10 +977,12 @@ func TestGithubClient_MergePullHandlesError(t *testing.T) {
 func TestGithubClient_MergePullCorrectMethod(t *testing.T) {
 	logger := logging.NewNoopLogger(t)
 	cases := map[string]struct {
-		allowMerge  bool
-		allowRebase bool
-		allowSquash bool
-		expMethod   string
+		allowMerge        bool
+		allowRebase       bool
+		allowSquash       bool
+		mergeMethodOption string
+		expMethod         string
+		expErr            string
 	}{
 		"all true": {
 			allowMerge:  true,
@@ -1012,6 +1014,59 @@ func TestGithubClient_MergePullCorrectMethod(t *testing.T) {
 			allowSquash: false,
 			expMethod:   "rebase",
 		},
+		"all true: merge with merge: overrided by command": {
+			allowMerge:        true,
+			allowRebase:       true,
+			allowSquash:       true,
+			mergeMethodOption: "merge",
+			expMethod:         "merge",
+		},
+		"all true: merge with rebase: overrided by command": {
+			allowMerge:        true,
+			allowRebase:       true,
+			allowSquash:       true,
+			mergeMethodOption: "rebase",
+			expMethod:         "rebase",
+		},
+		"all true: merge with squash: overrided by command": {
+			allowMerge:        true,
+			allowRebase:       true,
+			allowSquash:       true,
+			mergeMethodOption: "squash",
+			expMethod:         "squash",
+		},
+		"merge with merge: overrided by command: merge not allowed": {
+			allowMerge:        false,
+			allowRebase:       true,
+			allowSquash:       true,
+			mergeMethodOption: "merge",
+			expMethod:         "",
+			expErr:            "merge method is not allowed by repository settings",
+		},
+		"merge with rebase: overrided by command: rebase not allowed": {
+			allowMerge:        true,
+			allowRebase:       false,
+			allowSquash:       true,
+			mergeMethodOption: "rebase",
+			expMethod:         "",
+			expErr:            "rebase method is not allowed by repository settings",
+		},
+		"merge with squash: overrided by command: squash not allowed": {
+			allowMerge:        true,
+			allowRebase:       true,
+			allowSquash:       false,
+			mergeMethodOption: "squash",
+			expMethod:         "",
+			expErr:            "squash method is not allowed by repository settings",
+		},
+		"merge with unknown: overrided by command: unknown not exists": {
+			allowMerge:        true,
+			allowRebase:       true,
+			allowSquash:       true,
+			mergeMethodOption: "unknown",
+			expMethod:         "",
+			expErr:            "unknown method is unknown for GitHub, use one of them: [merge rebase squash]",
+		},
 	}
 
 	for name, c := range cases {
@@ -1086,9 +1141,14 @@ func TestGithubClient_MergePullCorrectMethod(t *testing.T) {
 					Num: 1,
 				}, models.PullRequestOptions{
 					DeleteSourceBranchOnMerge: false,
+					MergeMethod:               c.mergeMethodOption,
 				})
 
-			Ok(t, err)
+			if c.expErr == "" {
+				Ok(t, err)
+			} else {
+				ErrContains(t, c.expErr, err)
+			}
 		})
 	}
 }