diff --git a/.github/actions/gen-install-scripts/action.yml b/.github/actions/gen-install-scripts/action.yml
index 78c722e243..c9f08a323a 100644
--- a/.github/actions/gen-install-scripts/action.yml
+++ b/.github/actions/gen-install-scripts/action.yml
@@ -8,7 +8,7 @@ inputs:
     description: "Version of the Operator"
     required: true
   ENV:
-    description: "Kustomize patch name (enviroment configuration patch)"
+    description: "Kustomize patch name (environment configuration patch)"
     required: true
 runs:
   using: 'docker'
diff --git a/Makefile b/Makefile
index 7c5d3dfd78..f64fc7167c 100644
--- a/Makefile
+++ b/Makefile
@@ -498,3 +498,5 @@ gen-sdlc-checklist: envsubst docker-sbom ## Generate the SDLC checklist
 .PHONY: clear-e2e-leftovers
 clear-e2e-leftovers: ## Clear the e2e test leftovers quickly
 	git restore bundle* config deploy
+	cd helm-charts && git restore .
+	git submodule update helm-charts
diff --git a/test/e2e/helm_chart_test.go b/test/e2e/helm_chart_test.go
index 44548c5fdd..e31308e9fd 100644
--- a/test/e2e/helm_chart_test.go
+++ b/test/e2e/helm_chart_test.go
@@ -52,13 +52,13 @@ var _ = Describe("HELM charts", Ordered, func() {
 				Expect(err).Should(BeNil())
 				namespaceDeploymentJSON, err := json.MarshalIndent(namespaceDeployment, "", "  ")
 				Expect(err).Should(BeNil())
-				utils.SaveToFile("namespace-deployment.json", namespaceDeploymentJSON)
+				utils.SaveToFile("../../output/namespace-deployment.json", namespaceDeploymentJSON)
 
 				pod, err := k8s.GetAllDeploymentPods("mongodb-atlas-operator", data.Resources.Namespace)
 				Expect(err).Should(BeNil())
 				podJSON, err := json.MarshalIndent(pod, "", "  ")
 				Expect(err).Should(BeNil())
-				utils.SaveToFile("namespace-pod.json", podJSON)
+				utils.SaveToFile("../../output/namespace-pod.json", podJSON)
 
 				bytes, err := k8s.GetPodLogsByDeployment("mongodb-atlas-operator", config.DefaultOperatorNS, corev1.PodLogOptions{})
 				if err != nil {
diff --git a/test/helper/e2e/config/config.go b/test/helper/e2e/config/config.go
index 3f476dbf42..b9699cc121 100644
--- a/test/helper/e2e/config/config.go
+++ b/test/helper/e2e/config/config.go
@@ -10,7 +10,7 @@ const (
 	DefaultNamespacedOperatorConfig  = "../../deploy/namespaced/namespaced-config.yaml"
 
 	// Default names/path for tests coordinates
-	DataGenFolder            = "data/gen" // for generated configs
+	DataGenFolder            = "../helper/e2e/data/gen" // for generated configs
 	DefaultOperatorNS        = "mongodb-atlas-system"
 	DefaultOperatorName      = "mongodb-atlas-operator"
 	DefaultOperatorGlobalKey = "mongodb-atlas-operator-api-key"
@@ -42,4 +42,7 @@ const (
 
 	// GCP
 	FileNameSAGCP = "../../output/gcp_service_account.json"
+
+	// X509 auth test PEM key
+	PEMCertFileName = "../../output/x509cert.pem"
 )
diff --git a/test/helper/e2e/k8s/k8s.go b/test/helper/e2e/k8s/k8s.go
index 866e76455d..87b9a07e35 100644
--- a/test/helper/e2e/k8s/k8s.go
+++ b/test/helper/e2e/k8s/k8s.go
@@ -5,6 +5,7 @@ import (
 	"encoding/pem"
 	"fmt"
 	"os"
+	"path/filepath"
 
 	. "github.com/onsi/gomega"
 	"github.com/sethvargo/go-password/password"
@@ -14,16 +15,17 @@ import (
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/client-go/kubernetes/scheme"
 	"sigs.k8s.io/controller-runtime/pkg/client"
-	"sigs.k8s.io/controller-runtime/pkg/client/config"
+	k8scfg "sigs.k8s.io/controller-runtime/pkg/client/config"
 
 	akov2 "github.com/mongodb/mongodb-atlas-kubernetes/v2/pkg/api/v1"
 	"github.com/mongodb/mongodb-atlas-kubernetes/v2/pkg/api/v1/status"
 	"github.com/mongodb/mongodb-atlas-kubernetes/v2/pkg/controller/connectionsecret"
+	"github.com/mongodb/mongodb-atlas-kubernetes/v2/test/helper/e2e/config"
 	"github.com/mongodb/mongodb-atlas-kubernetes/v2/test/helper/e2e/utils"
 )
 
 func CreateNewClient() (client.Client, error) {
-	cfg, err := config.GetConfig()
+	cfg, err := k8scfg.GetConfig()
 	if err != nil {
 		return nil, err
 	}
@@ -252,10 +254,9 @@ func CreateCertificateX509(ctx context.Context, k8sClient client.Client, name, n
 		return fmt.Errorf("error generating x509 cert: %w", err)
 	}
 
-	certFileName := "x509cert.pem"
-	certFile, err := os.Create(certFileName)
+	certFile, err := os.Create(filepath.Clean(config.PEMCertFileName))
 	if err != nil {
-		return fmt.Errorf("failed to create file %s: %w", certFileName, err)
+		return fmt.Errorf("failed to create file %s: %w", config.PEMCertFileName, err)
 	}
 
 	err = pem.Encode(certFile, &pem.Block{
@@ -263,7 +264,7 @@ func CreateCertificateX509(ctx context.Context, k8sClient client.Client, name, n
 		Bytes: cert,
 	})
 	if err != nil {
-		return fmt.Errorf("failed to write data to %s: %w", certFileName, err)
+		return fmt.Errorf("failed to write data to %s: %w", config.PEMCertFileName, err)
 	}
 	err = certFile.Close()
 	if err != nil {
@@ -271,7 +272,7 @@ func CreateCertificateX509(ctx context.Context, k8sClient client.Client, name, n
 	}
 
 	var rawCert []byte
-	rawCert, err = os.ReadFile(certFileName)
+	rawCert, err = os.ReadFile(filepath.Clean(config.PEMCertFileName))
 	if err != nil {
 		return fmt.Errorf("failed to read cert file: %w", err)
 	}
@@ -282,7 +283,7 @@ func CreateCertificateX509(ctx context.Context, k8sClient client.Client, name, n
 			Namespace: ns,
 		},
 		Data: map[string][]byte{
-			certFileName: rawCert,
+			config.PEMCertFileName: rawCert,
 		},
 	}
 	certificateSecret.Labels = map[string]string{
diff --git a/test/helper/e2e/k8s/pod_logs.go b/test/helper/e2e/k8s/pod_logs.go
index bb9d668f66..2715653046 100644
--- a/test/helper/e2e/k8s/pod_logs.go
+++ b/test/helper/e2e/k8s/pod_logs.go
@@ -9,7 +9,7 @@ import (
 	corev1 "k8s.io/api/core/v1"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/client-go/kubernetes"
-	"sigs.k8s.io/controller-runtime/pkg/client/config"
+	k8scfg "sigs.k8s.io/controller-runtime/pkg/client/config"
 )
 
 func GetPodLogsByDeployment(deploymentName, deploymentNS string, options corev1.PodLogOptions) ([]byte, error) {
@@ -24,7 +24,7 @@ func GetPodLogsByDeployment(deploymentName, deploymentNS string, options corev1.
 }
 
 func GetPodLogs(options corev1.PodLogOptions, ns string, podName string) ([]byte, error) {
-	cfg, err := config.GetConfig()
+	cfg, err := k8scfg.GetConfig()
 	if err != nil {
 		return nil, fmt.Errorf("failed to get config: %w", err)
 	}
@@ -50,7 +50,7 @@ func GetPodLogs(options corev1.PodLogOptions, ns string, podName string) ([]byte
 }
 
 func GetAllDeploymentPods(deploymentName, deploymentNS string) ([]corev1.Pod, error) {
-	cfg, err := config.GetConfig()
+	cfg, err := k8scfg.GetConfig()
 	if err != nil {
 		return nil, fmt.Errorf("failed to get config: %w", err)
 	}
@@ -75,7 +75,7 @@ func GetAllDeploymentPods(deploymentName, deploymentNS string) ([]corev1.Pod, er
 }
 
 func GetDeployment(deploymentName, deploymentNS string) (*appsv1.Deployment, error) {
-	cfg, err := config.GetConfig()
+	cfg, err := k8scfg.GetConfig()
 	if err != nil {
 		return nil, fmt.Errorf("failed to get config: %w", err)
 	}