diff --git a/controller/sync.go b/controller/sync.go
index 34c12bdb5da3c..401d08bc56ea4 100644
--- a/controller/sync.go
+++ b/controller/sync.go
@@ -161,6 +161,12 @@ func (m *appStateManager) SyncAppState(app *v1alpha1.Application, state *v1alpha
 		state.Phase = common.OperationError
 		state.Message = fmt.Sprintf("Failed to load application project: %v", err)
 		return
+	} else if syncWindowPreventsSync(app, proj) {
+		// If the operation is currently running, simply let the user know the sync is blocked by a current sync window
+		if state.Phase == common.OperationRunning {
+			state.Message = "Sync operation blocked by sync window"
+		}
+		return
 	}
 
 	if app.Spec.HasMultipleSources() {
@@ -573,3 +579,12 @@ func delayBetweenSyncWaves(phase common.SyncPhase, wave int, finalWave bool) err
 	}
 	return nil
 }
+
+func syncWindowPreventsSync(app *v1alpha1.Application, proj *v1alpha1.AppProject) bool {
+	window := proj.Spec.SyncWindows.Matches(app)
+	isManual := false
+	if app.Status.OperationState != nil {
+		isManual = !app.Status.OperationState.Operation.InitiatedBy.Automated
+	}
+	return !window.CanSync(isManual)
+}
diff --git a/controller/sync_test.go b/controller/sync_test.go
index 309f846ca6460..f9bd81c1c138a 100644
--- a/controller/sync_test.go
+++ b/controller/sync_test.go
@@ -254,6 +254,75 @@ func TestAppStateManager_SyncAppState(t *testing.T) {
 	})
 }
 
+func TestSyncWindowDeniesSync(t *testing.T) {
+	type fixture struct {
+		project     *v1alpha1.AppProject
+		application *v1alpha1.Application
+		controller  *ApplicationController
+	}
+
+	setup := func() *fixture {
+		app := newFakeApp()
+		app.Status.OperationState = nil
+		app.Status.History = nil
+
+		project := &v1alpha1.AppProject{
+			ObjectMeta: v1.ObjectMeta{
+				Namespace: test.FakeArgoCDNamespace,
+				Name:      "default",
+			},
+			Spec: v1alpha1.AppProjectSpec{
+				SyncWindows: v1alpha1.SyncWindows{{
+					Kind:         "deny",
+					Schedule:     "0 0 * * *",
+					Duration:     "24h",
+					Clusters:     []string{"*"},
+					Namespaces:   []string{"*"},
+					Applications: []string{"*"},
+				}},
+			},
+		}
+		data := fakeData{
+			apps: []runtime.Object{app, project},
+			manifestResponse: &apiclient.ManifestResponse{
+				Manifests: []string{},
+				Namespace: test.FakeDestNamespace,
+				Server:    test.FakeClusterURL,
+				Revision:  "abc123",
+			},
+			managedLiveObjs: make(map[kube.ResourceKey]*unstructured.Unstructured),
+		}
+		ctrl := newFakeController(&data, nil)
+
+		return &fixture{
+			project:     project,
+			application: app,
+			controller:  ctrl,
+		}
+	}
+
+	t.Run("will keep the sync progressing if a sync window prevents the sync", func(t *testing.T) {
+		// given a project with an active deny sync window and an operation in progress
+		t.Parallel()
+		f := setup()
+		opMessage := "Sync operation blocked by sync window"
+
+		opState := &v1alpha1.OperationState{Operation: v1alpha1.Operation{
+			Sync: &v1alpha1.SyncOperation{
+				Source: &v1alpha1.ApplicationSource{},
+			}},
+			Phase: common.OperationRunning,
+		}
+		// when
+		f.controller.appStateManager.SyncAppState(f.application, opState)
+
+		//then
+		assert.Equal(t, common.OperationRunning, opState.Phase)
+		assert.Contains(t, opState.Message, opMessage)
+	})
+
+}
+
 func TestNormalizeTargetResources(t *testing.T) {
 	type fixture struct {
 		comparisonResult *comparisonResult