diff --git a/pkg/controller/jenkins/groovy/groovy.go b/pkg/controller/jenkins/groovy/groovy.go
index 5284f176..ec9823ed 100644
--- a/pkg/controller/jenkins/groovy/groovy.go
+++ b/pkg/controller/jenkins/groovy/groovy.go
@@ -55,12 +55,22 @@ func (g *Groovy) EnsureSingle(source, name, hash, groovyScript string) (requeue
 		return true, err
 	}
 
-	g.jenkins.Status.AppliedGroovyScripts = append(g.jenkins.Status.AppliedGroovyScripts, v1alpha2.AppliedGroovyScript{
+	var appliedGroovyScripts []v1alpha2.AppliedGroovyScript
+
+	for _, ags := range g.jenkins.Status.AppliedGroovyScripts {
+		if ags.ConfigurationType != g.configurationType && ags.Source != source && ags.Name != name {
+			appliedGroovyScripts = append(appliedGroovyScripts, ags)
+		}
+	}
+	appliedGroovyScripts = append(appliedGroovyScripts, v1alpha2.AppliedGroovyScript{
 		ConfigurationType: g.configurationType,
 		Source:            source,
 		Name:              name,
 		Hash:              hash,
 	})
+
+	g.jenkins.Status.AppliedGroovyScripts = appliedGroovyScripts
+
 	return true, g.k8sClient.Update(context.TODO(), g.jenkins)
 }
 
diff --git a/pkg/controller/jenkins/groovy/groovy_test.go b/pkg/controller/jenkins/groovy/groovy_test.go
index 14286764..1650020a 100644
--- a/pkg/controller/jenkins/groovy/groovy_test.go
+++ b/pkg/controller/jenkins/groovy/groovy_test.go
@@ -113,6 +113,70 @@ func TestGroovy_EnsureSingle(t *testing.T) {
 		assert.Equal(t, source, jenkins.Status.AppliedGroovyScripts[0].Source)
 		assert.Equal(t, groovyScriptName, jenkins.Status.AppliedGroovyScripts[0].Name)
 	})
+	t.Run("execute script with new version", func(t *testing.T) {
+		anotherHash := "hash1"
+		// given
+		jenkins := &v1alpha2.Jenkins{
+			ObjectMeta: metav1.ObjectMeta{
+				Name:      jenkinsName,
+				Namespace: namespace,
+			},
+		}
+		err := v1alpha2.SchemeBuilder.AddToScheme(scheme.Scheme)
+		require.NoError(t, err)
+		fakeClient := fake.NewFakeClient()
+		err = fakeClient.Create(ctx, jenkins)
+		require.NoError(t, err)
+
+		ctrl := gomock.NewController(t)
+		defer ctrl.Finish()
+		jenkinsClient := jenkinsclient.NewMockJenkins(ctrl)
+
+		jenkinsClient.EXPECT().ExecuteScript(groovyScript).Return("logs", nil)
+		jenkinsClient.EXPECT().ExecuteScript(groovyScript).Return("logs", nil)
+		jenkinsClient.EXPECT().ExecuteScript(groovyScript).Return("logs", nil)
+
+		groovyClient := New(jenkinsClient, fakeClient, log.Log, jenkins, configurationType, emptyCustomization)
+
+		// when
+		requeue, err := groovyClient.EnsureSingle(source, groovyScriptName, hash, groovyScript)
+
+		// then
+		require.NoError(t, err)
+		assert.True(t, requeue)
+		err = fakeClient.Get(ctx, types.NamespacedName{Name: jenkins.Name, Namespace: jenkins.Namespace}, jenkins)
+		require.NoError(t, err)
+		assert.Equal(t, 1, len(jenkins.Status.AppliedGroovyScripts))
+		assert.Equal(t, configurationType, jenkins.Status.AppliedGroovyScripts[0].ConfigurationType)
+		assert.Equal(t, hash, jenkins.Status.AppliedGroovyScripts[0].Hash)
+		assert.Equal(t, source, jenkins.Status.AppliedGroovyScripts[0].Source)
+		assert.Equal(t, groovyScriptName, jenkins.Status.AppliedGroovyScripts[0].Name)
+
+		// Update with new hash
+		requeue, err = groovyClient.EnsureSingle(source, groovyScriptName, anotherHash, groovyScript)
+		require.NoError(t, err)
+		assert.True(t, requeue)
+
+		err = fakeClient.Get(ctx, types.NamespacedName{Name: jenkins.Name, Namespace: jenkins.Namespace}, jenkins)
+		require.NoError(t, err)
+		assert.Equal(t, 1, len(jenkins.Status.AppliedGroovyScripts))
+		assert.Equal(t, configurationType, jenkins.Status.AppliedGroovyScripts[0].ConfigurationType)
+		assert.Equal(t, anotherHash, jenkins.Status.AppliedGroovyScripts[0].Hash)
+		assert.Equal(t, source, jenkins.Status.AppliedGroovyScripts[0].Source)
+		assert.Equal(t, groovyScriptName, jenkins.Status.AppliedGroovyScripts[0].Name)
+
+		requeue, err = groovyClient.EnsureSingle(source, groovyScriptName, hash, groovyScript)
+		require.NoError(t, err)
+		assert.True(t, requeue)
+
+		err = fakeClient.Get(ctx, types.NamespacedName{Name: jenkins.Name, Namespace: jenkins.Namespace}, jenkins)
+		require.NoError(t, err)
+		assert.Equal(t, 1, len(jenkins.Status.AppliedGroovyScripts))
+		assert.Equal(t, configurationType, jenkins.Status.AppliedGroovyScripts[0].ConfigurationType)
+		assert.Equal(t, hash, jenkins.Status.AppliedGroovyScripts[0].Hash)
+		assert.Equal(t, source, jenkins.Status.AppliedGroovyScripts[0].Source)
+		assert.Equal(t, groovyScriptName, jenkins.Status.AppliedGroovyScripts[0].Name)
+	})
 	t.Run("execute script fails", func(t *testing.T) {
 		// given
 		jenkins := &v1alpha2.Jenkins{
diff --git a/test/e2e/configuration_test.go b/test/e2e/configuration_test.go
index 7e0af964..0beae099 100644
--- a/test/e2e/configuration_test.go
+++ b/test/e2e/configuration_test.go
@@ -6,18 +6,18 @@ import (
 	"testing"
 
 	"github.com/jenkinsci/kubernetes-operator/pkg/apis/jenkins/v1alpha2"
-	"github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/groovy"
 	jenkinsclient "github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/client"
 	"github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/configuration/base"
 	"github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/configuration/base/resources"
+	"github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/groovy"
 	"github.com/jenkinsci/kubernetes-operator/pkg/controller/jenkins/plugins"
 
-	corev1 "k8s.io/api/core/v1"
-	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"github.com/bndr/gojenkins"
-	"k8s.io/apimachinery/pkg/api/resource"
 	framework "github.com/operator-framework/operator-sdk/pkg/test"
 	"github.com/stretchr/testify/assert"
+	corev1 "k8s.io/api/core/v1"
+	"k8s.io/apimachinery/pkg/api/resource"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 )
 
 func TestConfiguration(t *testing.T) {