diff --git a/integrationtests/cli/apply/apply_online_test.go b/integrationtests/cli/apply/apply_online_test.go
index d12654b82e..a8d1d7025c 100644
--- a/integrationtests/cli/apply/apply_online_test.go
+++ b/integrationtests/cli/apply/apply_online_test.go
@@ -5,6 +5,8 @@
 package apply
 
 import (
+	"time"
+
 	"go.uber.org/mock/gomock"
 
 	. "github.com/onsi/ginkgo/v2"
@@ -116,4 +118,70 @@ data:
 
 	})
 
+	When("a bundle to be created already exists and is marked for deletion", func() {
+		BeforeEach(func() {
+			ts := metav1.NewTime(time.Now())
+			name = "labels_update"
+			dirs = []string{cli.AssetsPath + "labels_update"}
+			//bundle in the cluster
+			oldBundle = &fleet.Bundle{
+				ObjectMeta: metav1.ObjectMeta{
+					Namespace:         "foo",
+					Name:              "test_labels",
+					DeletionTimestamp: &ts, // as long as it's non-nil
+				},
+			}
+			// bundle in the cm.yaml file; some values are autofilled in the implementation (this is why there are not only the labels)
+			newBundle = &fleet.Bundle{
+				ObjectMeta: metav1.ObjectMeta{
+					Labels: map[string]string{
+						"new": "fleet-label2",
+					},
+					Namespace: "foo",
+					Name:      "test_labels",
+				},
+				Spec: fleet.BundleSpec{
+					Resources: []fleet.BundleResource{
+						{
+							Name: "cm.yaml",
+							Content: `apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: cm3
+data:
+  test: "value23"
+`,
+						},
+					},
+					Targets: []fleet.BundleTarget{
+						{
+							Name:         "default",
+							ClusterGroup: "default",
+						},
+					},
+				},
+			}
+		})
+
+		It("does not update the bundle", func() {
+			// no expected call to update nor updateStatus, as the existing bundle is being deleted
+			err := fleetApplyOnline(getter, name, dirs, options)
+			Expect(err).To(HaveOccurred())
+			Expect(err.Error()).To(ContainSubstring("is being deleted"))
+		})
+
+		It("does not update an OCI bundle", func() {
+			// no expected call to update nor updateStatus, as the existing bundle is being deleted
+			bkp := options.OCIRegistry.Reference
+			options.OCIRegistry.Reference = "oci://foo" // non-empty
+
+			defer func() { options.OCIRegistry.Reference = bkp }()
+
+			err := fleetApplyOnline(getter, name, dirs, options)
+			Expect(err).To(HaveOccurred())
+			Expect(err.Error()).To(ContainSubstring("is being deleted"))
+		})
+
+	})
+
 })
diff --git a/internal/cmd/cli/apply/apply.go b/internal/cmd/cli/apply/apply.go
index 17a13f1d1a..f44cb22dc3 100644
--- a/internal/cmd/cli/apply/apply.go
+++ b/internal/cmd/cli/apply/apply.go
@@ -247,6 +247,13 @@ func Dir(ctx context.Context, client Getter, name, baseDir string, opts *Options
 			return err
 		}
 
+		// We need to exit early if the bundle is being deleted
+		if tmp, err := c.Fleet.Bundle().Get(bundle.Namespace, bundle.Name, metav1.GetOptions{}); err == nil {
+			if tmp.DeletionTimestamp != nil {
+				return fmt.Errorf("the bundle %q is being deleted, cannot create during a delete operation", bundle.Name)
+			}
+		}
+
 		h, data, err := helmvalues.ExtractValues(bundle)
 		if err != nil {
 			return err
@@ -324,6 +331,11 @@ func save(c *client.Client, bundle *fleet.Bundle) (*fleet.Bundle, error) {
 		}
 		logrus.Infof("created (bundle): %s/%s", bundle.Namespace, bundle.Name)
 	} else {
+		// We cannot update a bundle that is going to be deleted, our update would be lost
+		if obj.DeletionTimestamp != nil {
+			return bundle, fmt.Errorf("the bundle %q is being deleted", bundle.Name)
+		}
+
 		obj.Spec = bundle.Spec
 		obj.Annotations = bundle.Annotations
 		obj.Labels = bundle.Labels
@@ -391,6 +403,10 @@ func saveOCIBundle(ctx context.Context, c *client.Client, bundle *fleet.Bundle,
 		}
 		logrus.Infof("createOrUpdate (oci secret): %s/%s", obj.Namespace, obj.Name)
 	} else {
+		if obj.DeletionTimestamp != nil {
+			return bundle, fmt.Errorf("the bundle %q is being deleted", bundle.Name)
+		}
+
 		obj.Spec = bundle.Spec
 		obj.Annotations = bundle.Annotations
 		obj.Labels = bundle.Labels