diff --git a/endpoint/endpoint.go b/endpoint/endpoint.go
index f7af843f6..9c7107a37 100644
--- a/endpoint/endpoint.go
+++ b/endpoint/endpoint.go
@@ -374,3 +374,24 @@ type DNSEndpointList struct {
 	metav1.ListMeta `json:"metadata,omitempty"`
 	Items           []DNSEndpoint `json:"items"`
 }
+
+// RemoveDuplicates returns a slice holding the unique endpoints.
+// This function doesn't contemplate the Targets of an Endpoint
+// as part of the primary Key
+func RemoveDuplicates(endpoints []*Endpoint) []*Endpoint {
+	visited := make(map[EndpointKey]struct{})
+	result := []*Endpoint{}
+
+	for _, ep := range endpoints {
+		key := ep.Key()
+
+		if _, found := visited[key]; !found {
+			result = append(result, ep)
+			visited[key] = struct{}{}
+		} else {
+			log.Debugf(`Skipping duplicated endpoint: %v`, ep)
+		}
+	}
+
+	return result
+}
diff --git a/endpoint/endpoint_test.go b/endpoint/endpoint_test.go
index a3b3399cf..0d87c2bbe 100644
--- a/endpoint/endpoint_test.go
+++ b/endpoint/endpoint_test.go
@@ -252,3 +252,136 @@ func TestIsOwnedBy(t *testing.T) {
 		})
 	}
 }
+
+func TestDuplicatedEndpointsWithSimpleZone(t *testing.T) {
+	foo1 := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	foo2 := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	bar := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "bar",
+		},
+	}
+
+	type args struct {
+		eps []*Endpoint
+	}
+	tests := []struct {
+		name string
+		args args
+		want []*Endpoint
+	}{
+		{
+			name: "filter values",
+			args: args{
+				eps: []*Endpoint{
+					foo1,
+					foo2,
+					bar,
+				},
+			},
+			want: []*Endpoint{
+				foo1,
+			},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := RemoveDuplicates(tt.args.eps); !reflect.DeepEqual(got, tt.want) {
+				t.Errorf("RemoveDuplicates() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestDuplicatedEndpointsWithOverlappingZones(t *testing.T) {
+	foo1 := &Endpoint{
+		DNSName:    "internal.foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	foo2 := &Endpoint{
+		DNSName:    "internal.foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	foo3 := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	foo4 := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "foo",
+		},
+	}
+	bar := &Endpoint{
+		DNSName:    "internal.foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "bar",
+		},
+	}
+	bar2 := &Endpoint{
+		DNSName:    "foo.com",
+		RecordType: RecordTypeA,
+		Labels: Labels{
+			OwnerLabelKey: "bar",
+		},
+	}
+
+	type args struct {
+		eps []*Endpoint
+	}
+	tests := []struct {
+		name string
+		args args
+		want []*Endpoint
+	}{
+		{
+			name: "filter values",
+			args: args{
+				eps: []*Endpoint{
+					foo1,
+					foo2,
+					foo3,
+					foo4,
+					bar,
+					bar2,
+				},
+			},
+			want: []*Endpoint{
+				foo1,
+				foo3,
+			},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := RemoveDuplicates(tt.args.eps); !reflect.DeepEqual(got, tt.want) {
+				t.Errorf("RemoveDuplicates() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
diff --git a/plan/plan.go b/plan/plan.go
index b4100328d..d0ca7f96a 100644
--- a/plan/plan.go
+++ b/plan/plan.go
@@ -252,6 +252,7 @@ func (p *Plan) Calculate() *Plan {
 	// filter out updates this external dns does not have ownership claim over
 	if p.OwnerID != "" {
 		changes.Delete = endpoint.FilterEndpointsByOwnerID(p.OwnerID, changes.Delete)
+		changes.Delete = endpoint.RemoveDuplicates(changes.Delete)
 		changes.UpdateOld = endpoint.FilterEndpointsByOwnerID(p.OwnerID, changes.UpdateOld)
 		changes.UpdateNew = endpoint.FilterEndpointsByOwnerID(p.OwnerID, changes.UpdateNew)
 	}