diff --git a/config/crd/bases/styra.bankdata.dk_libraries.yaml b/config/crd/bases/styra.bankdata.dk_libraries.yaml
index f6018f6d..f8281cce 100644
--- a/config/crd/bases/styra.bankdata.dk_libraries.yaml
+++ b/config/crd/bases/styra.bankdata.dk_libraries.yaml
@@ -3,7 +3,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.19.0
+    controller-gen.kubebuilder.io/version: v0.20.0
   name: libraries.styra.bankdata.dk
 spec:
   group: styra.bankdata.dk
diff --git a/config/crd/bases/styra.bankdata.dk_systems.yaml b/config/crd/bases/styra.bankdata.dk_systems.yaml
index cb621b93..555ad550 100644
--- a/config/crd/bases/styra.bankdata.dk_systems.yaml
+++ b/config/crd/bases/styra.bankdata.dk_systems.yaml
@@ -3,7 +3,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.19.0
+    controller-gen.kubebuilder.io/version: v0.20.0
   name: systems.styra.bankdata.dk
 spec:
   group: styra.bankdata.dk
diff --git a/docs/apis/styra/v1alpha1.md b/docs/apis/styra/v1alpha1.md
index 1f0e8fb7..85b5cee0 100644
--- a/docs/apis/styra/v1alpha1.md
+++ b/docs/apis/styra/v1alpha1.md
@@ -458,5 +458,5 @@ GitRepo
 <hr/>
 <p><em>
 Generated with <code>gen-crd-api-reference-docs</code>
-on git commit <code>4901ef1</code>.
+on git commit <code>237726c</code>.
 </em></p>
diff --git a/docs/apis/styra/v1beta1.md b/docs/apis/styra/v1beta1.md
index 84a95cd0..9831ff7d 100644
--- a/docs/apis/styra/v1beta1.md
+++ b/docs/apis/styra/v1beta1.md
@@ -1424,5 +1424,5 @@ System.</p>
 <hr/>
 <p><em>
 Generated with <code>gen-crd-api-reference-docs</code>
-on git commit <code>4901ef1</code>.
+on git commit <code>237726c</code>.
 </em></p>
diff --git a/internal/controller/styra/system_controller.go b/internal/controller/styra/system_controller.go
index 4af6c963..4518b163 100644
--- a/internal/controller/styra/system_controller.go
+++ b/internal/controller/styra/system_controller.go
@@ -854,8 +854,7 @@ func (r *SystemReconciler) reconcileSystemSource(
 	}
 	if system.Spec.SourceControl.Origin.Commit != "" {
 		gitConfig.Commit = system.Spec.SourceControl.Origin.Commit
-	}
-	if system.Spec.SourceControl.Origin.Reference != "" {
+	} else if system.Spec.SourceControl.Origin.Reference != "" {
 		gitConfig.Reference = system.Spec.SourceControl.Origin.Reference
 	}
 	if system.Spec.SourceControl.Origin.Path != "" {
diff --git a/test/integration/controller/system_controller_test.go b/test/integration/controller/system_controller_test.go
index fc8bf798..7313c567 100644
--- a/test/integration/controller/system_controller_test.go
+++ b/test/integration/controller/system_controller_test.go
@@ -2537,6 +2537,7 @@ var _ = ginkgo.Describe("SystemReconciler.ReconcileOCPSystem", ginkgo.Label("int
 		sourceControl := styrav1beta1.SourceControl{
 			Origin: styrav1beta1.GitRepo{
 				URL:       "https://github.com/test/repo.git",
+				Commit:    "0123456789abcdef",
 				Reference: "refs/heads/master",
 				Path:      "policy",
 			},
@@ -2595,7 +2596,7 @@ var _ = ginkgo.Describe("SystemReconciler.ReconcileOCPSystem", ginkgo.Label("int
 			Name: "default-ocp-system",
 			Git: &ocp.GitConfig{
 				Repo:          "https://github.com/test/repo.git",
-				Reference:     "refs/heads/master",
+				Commit:        "0123456789abcdef",
 				Path:          "policy",
 				CredentialID:  expectedGitCredentialsID,
 				IncludedFiles: []string{"*.rego"},
@@ -2653,7 +2654,7 @@ var _ = ginkgo.Describe("SystemReconciler.ReconcileOCPSystem", ginkgo.Label("int
 			Name: "default-ocp-system",
 			Git: &ocp.GitConfig{
 				Repo:          "https://github.com/test/repo.git",
-				Reference:     "refs/heads/master",
+				Commit:        "0123456789abcdef",
 				Path:          "policy",
 				CredentialID:  expectedGitCredentialsID,
 				IncludedFiles: []string{"*.rego"},
@@ -2705,7 +2706,7 @@ var _ = ginkgo.Describe("SystemReconciler.ReconcileOCPSystem", ginkgo.Label("int
 			Name: "default-ocp-system",
 			Git: &ocp.GitConfig{
 				Repo:          "https://github.com/test/repo.git",
-				Reference:     "refs/heads/master",
+				Commit:        "0123456789abcdef",
 				Path:          "policy",
 				CredentialID:  expectedGitCredentialsID,
 				IncludedFiles: []string{"*.rego"},