diff --git a/lib/services/reconciler.go b/lib/services/reconciler.go
index 7a22bd974de..70376f30557 100644
--- a/lib/services/reconciler.go
+++ b/lib/services/reconciler.go
@@ -137,6 +137,8 @@ func (r *GenericReconciler[K, T]) Reconcile(ctx context.Context) error {
 		}
 	}
 
+	// TODO(zmb3): with a large number of resources, this can return a lengthy
+	// error message that is difficult to parse
 	return trace.NewAggregate(errs...)
 }
 
@@ -154,6 +156,10 @@ func (r *GenericReconciler[K, T]) processRegisteredResource(ctx context.Context,
 	}
 	r.logger.InfoContext(ctx, "Resource was removed, deleting", "kind", kind, "name", key)
 	if err := r.cfg.OnDelete(ctx, registered); err != nil {
+		if trace.IsNotFound(err) {
+			r.logger.Log(ctx, logutils.TraceLevel, "Failed to delete resource", "kind", kind, "name", key, "err", err)
+			return nil
+		}
 		return trace.Wrap(err, "failed to delete  %v %v", kind, key)
 	}
 
@@ -216,6 +222,10 @@ func (r *GenericReconciler[K, T]) processNewResource(ctx context.Context, curren
 		}
 		r.logger.InfoContext(ctx, "Existing resource updated and no longer matches, deleting", "name", key)
 		if err := r.cfg.OnDelete(ctx, registered); err != nil {
+			if trace.IsNotFound(err) {
+				r.logger.Log(ctx, logutils.TraceLevel, "Failed to delete resource", "kind", kind, "name", key, "err", err)
+				return nil
+			}
 			return trace.Wrap(err, "failed to delete %v %v", kind, key)
 		}
 		return nil
diff --git a/lib/services/reconciler_test.go b/lib/services/reconciler_test.go
index ad97fb61c90..aec02937619 100644
--- a/lib/services/reconciler_test.go
+++ b/lib/services/reconciler_test.go
@@ -23,6 +23,7 @@ import (
 	"maps"
 	"testing"
 
+	"github.com/gravitational/trace"
 	"github.com/stretchr/testify/require"
 
 	headerv1 "github.com/gravitational/teleport/api/gen/proto/go/teleport/header/v1"
@@ -106,6 +107,26 @@ func TestReconciler(t *testing.T) {
 			registeredResources: []testResource{makeDynamicResource("res1", nil)},
 			onDeleteCalls:       []testResource{makeDynamicResource("res1", nil)},
 		},
+		{
+			description: "removing a resource that doesn't exist is not an error",
+			selectors: []ResourceMatcher{{
+				Labels: types.Labels{"foo": []string{"bar"}},
+			}},
+			// Note the label change below. This means the resource no longer matches and should be removed.
+			registeredResources: []testResource{makeDynamicResource("res1", map[string]string{"foo": "bar"})},
+			newResources:        []testResource{makeDynamicResource("res1", map[string]string{"baz": "quux"})},
+
+			// Simulate the resource having already expired from the backend.
+			configure: func(cfg *ReconcilerConfig[testResource]) {
+				originalDelete := cfg.OnDelete
+				cfg.OnDelete = func(ctx context.Context, tr testResource) error {
+					originalDelete(ctx, tr)
+					return trace.NotFound("resource does not exist")
+				}
+			},
+
+			onDeleteCalls: []testResource{makeDynamicResource("res1", map[string]string{"foo": "bar"})},
+		},
 		{
 			description: "resource with updated matching labels should be updated",
 			selectors: []ResourceMatcher{{