diff --git a/cmd/root.go b/cmd/root.go
index f7caa54fd..d3ef3fce9 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -12,7 +12,6 @@ import (
 
 	"github.com/getsentry/sentry-go"
 	"github.com/go-errors/errors"
-	"github.com/mitchellh/mapstructure"
 	"github.com/spf13/afero"
 	"github.com/spf13/cobra"
 	"github.com/spf13/viper"
@@ -223,18 +222,8 @@ func recoverAndExit() {
 
 func init() {
 	cobra.OnInitialize(func() {
-		// Allow overriding config object with automatic env
-		// Ref: https://github.com/spf13/viper/issues/761
-		envKeysMap := map[string]interface{}{}
-		dec, err := mapstructure.NewDecoder(&mapstructure.DecoderConfig{
-			Result:               &envKeysMap,
-			IgnoreUntaggedFields: true,
-		})
-		cobra.CheckErr(err)
-		cobra.CheckErr(dec.Decode(utils.Config))
-		cobra.CheckErr(viper.MergeConfigMap(envKeysMap))
 		viper.SetEnvPrefix("SUPABASE")
-		viper.SetEnvKeyReplacer(strings.NewReplacer("-", "_", ".", "_"))
+		viper.SetEnvKeyReplacer(strings.NewReplacer("-", "_"))
 		viper.AutomaticEnv()
 	})
 
diff --git a/pkg/config/config.go b/pkg/config/config.go
index 3bf566bb1..8914dcac0 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -28,6 +28,7 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/golang-jwt/jwt/v5"
 	"github.com/joho/godotenv"
+	"github.com/mitchellh/mapstructure"
 	"github.com/spf13/viper"
 	"golang.org/x/mod/semver"
 
@@ -136,13 +137,13 @@ type (
 		EdgeRuntime  edgeRuntime    `toml:"edge_runtime"`
 		Functions    FunctionConfig `toml:"functions"`
 		Analytics    analytics      `toml:"analytics"`
-		Experimental experimental   `toml:"experimental" mapstructure:"-"`
+		Experimental experimental   `toml:"experimental"`
 	}
 
 	config struct {
-		baseConfig
-		Overrides map[string]interface{} `toml:"remotes"`
-		Remotes   map[string]baseConfig  `toml:"-"`
+		baseConfig `mapstructure:",squash"`
+		Overrides  map[string]interface{} `toml:"remotes"`
+		Remotes    map[string]baseConfig  `toml:"-"`
 	}
 
 	db struct {
@@ -587,6 +588,29 @@ func (c *config) Eject(w io.Writer) error {
 	return nil
 }
 
+func (c *config) loadFromEnv() error {
+	// Allow overriding base config object with automatic env
+	// Ref: https://github.com/spf13/viper/issues/761
+	envKeysMap := map[string]interface{}{}
+	if dec, err := mapstructure.NewDecoder(&mapstructure.DecoderConfig{
+		Result:               &envKeysMap,
+		IgnoreUntaggedFields: true,
+	}); err != nil {
+		return errors.Errorf("failed to create decoder: %w", err)
+	} else if err := dec.Decode(c.baseConfig); err != nil {
+		return errors.Errorf("failed to decode env: %w", err)
+	}
+	v := viper.New()
+	v.SetEnvKeyReplacer(strings.NewReplacer(".", "_"))
+	v.AutomaticEnv()
+	if err := v.MergeConfigMap(envKeysMap); err != nil {
+		return errors.Errorf("failed to merge config: %w", err)
+	} else if err := v.Unmarshal(c); err != nil {
+		return errors.Errorf("failed to parse env to config: %w", err)
+	}
+	return nil
+}
+
 func (c *config) Load(path string, fsys fs.FS) error {
 	builder := NewPathBuilder(path)
 	// Load default values
@@ -614,9 +638,8 @@ func (c *config) Load(path string, fsys fs.FS) error {
 	// Load secrets from .env file
 	if err := loadDefaultEnv(); err != nil {
 		return err
-	}
-	if err := viper.Unmarshal(c); err != nil {
-		return errors.Errorf("failed to parse env to config: %w", err)
+	} else if err := c.loadFromEnv(); err != nil {
+		return err
 	}
 	// Generate JWT tokens
 	if len(c.Auth.AnonKey) == 0 {
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index af3ab9563..bef3df123 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -341,3 +341,15 @@ func TestLoadSeedPaths(t *testing.T) {
 		assert.Empty(t, config.SqlPaths)
 	})
 }
+
+func TestLoadEnv(t *testing.T) {
+	t.Setenv("AUTH_JWT_SECRET", "test-secret")
+	t.Setenv("DB_ROOT_KEY", "test-root-key")
+	config := NewConfig()
+	// Run test
+	err := config.loadFromEnv()
+	// Check error
+	assert.NoError(t, err)
+	assert.Equal(t, "test-secret", config.Auth.JwtSecret)
+	assert.Equal(t, "test-root-key", config.Db.RootKey)
+}