diff --git a/pkg/jobs/jobs.go b/pkg/jobs/jobs.go
index 860c08d71..e050cc6d6 100644
--- a/pkg/jobs/jobs.go
+++ b/pkg/jobs/jobs.go
@@ -47,7 +47,12 @@ func Start() {
 		}
 	}
 
-	for _, j := range []*job.Job{topologyJobs.CleanupDeletedTopologyComponents, topologyJobs.SyncTopology, canaryJobs.SyncCanaryJobs, canaryJobs.CleanupDeletedCanaryChecks, dutyQuery.SyncComponentCacheJob} {
+	miscJobs := []*job.Job{
+		topologyJobs.CleanupDeletedTopologyComponents, topologyJobs.SyncTopology,
+		topologyJobs.TopologyCRDReconcile, canaryJobs.SyncCanaryJobs,
+		canaryJobs.CleanupDeletedCanaryChecks, dutyQuery.SyncComponentCacheJob,
+	}
+	for _, j := range miscJobs {
 		job := j
 		job.Context = context.DefaultContext
 		if err := job.AddToScheduler(FuncScheduler); err != nil {
diff --git a/pkg/jobs/topology/topology_jobs.go b/pkg/jobs/topology/topology_jobs.go
index 094ab4a0c..cff43db35 100644
--- a/pkg/jobs/topology/topology_jobs.go
+++ b/pkg/jobs/topology/topology_jobs.go
@@ -3,6 +3,7 @@ package topology
 import (
 	"fmt"
 	"reflect"
+	"slices"
 	"sync"
 
 	canaryCtx "github.com/flanksource/canary-checker/api/context"
@@ -17,6 +18,9 @@ import (
 	"github.com/flanksource/duty/job"
 	"github.com/flanksource/duty/models"
 	"github.com/robfig/cron/v3"
+	"github.com/samber/lo"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
+	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
 )
 
 var TopologyScheduler = cron.New()
@@ -157,3 +161,51 @@ var CleanupDeletedTopologyComponents = &job.Job{
 		return nil
 	},
 }
+
+var TopologyCRDReconcile = &job.Job{
+	Name:       "TopologyCRDReconcile",
+	Schedule:   "@every 8h",
+	Singleton:  true,
+	JobHistory: true,
+	Retention:  job.RetentionBalanced,
+	Fn: func(ctx job.JobRuntime) error {
+		var topologies []models.Topology
+
+		if err := ctx.DB().
+			Select("id", "name", "namespace").
+			Where("source IN (?, ?)", models.SourceCRD, models.SourceTopology).
+			Where(duty.LocalFilter).
+			Find(&topologies).Error; err != nil {
+			return err
+		}
+
+		client, err := ctx.KubernetesDynamicClient().GetClientByKind("Topology")
+		if err != nil {
+			return fmt.Errorf("error creating dynamic client for Topology: %w", err)
+		}
+
+		objs, err := client.List(ctx, metav1.ListOptions{})
+		if err != nil {
+			return fmt.Errorf("error listing Topology kind: %w", err)
+		}
+		k8sIDs := lo.Map(objs.Items, func(obj unstructured.Unstructured, _ int) string { return string(obj.GetUID()) })
+		if len(k8sIDs) == 0 {
+			// a misconfiguration or intermittent error could cause unnecessary deletion of all topologies
+			ctx.Warnf("Skipping topology CRD cleanup due to zero topologies returned")
+			return nil
+		}
+		for _, t := range topologies {
+			if !slices.Contains(k8sIDs, t.ID.String()) {
+				// id mismatch or object not found in k8s, delete current topology
+				if err := db.DeleteTopology(ctx.DB(), t.ID.String()); err != nil {
+					ctx.History.AddErrorf("error deleting topology[%s]: %v", t.ID, err)
+					continue
+				}
+				DeleteTopologyJob(t.ID.String())
+			}
+
+			ctx.History.IncrSuccess()
+		}
+		return nil
+	},
+}