diff --git a/cli/cmd/install.go b/cli/cmd/install.go
index f8173b91a8..8d31b7f9c2 100644
--- a/cli/cmd/install.go
+++ b/cli/cmd/install.go
@@ -205,7 +205,6 @@ func validateUserInputProfiles(tier common.OdigosTier) {
 }
 
 func createOdigosConfig(odigosTier common.OdigosTier) common.OdigosConfiguration {
-	fullIgnoredNamespaces := utils.MergeDefaultIgnoreWithUserInput(userInputIgnoredNamespaces, consts.SystemNamespaces)
 	fullIgnoredContainers := utils.MergeDefaultIgnoreWithUserInput(userInputIgnoredContainers, consts.IgnoredContainers)
 
 	selectedProfiles := []common.ProfileName{}
@@ -218,7 +217,7 @@ func createOdigosConfig(odigosTier common.OdigosTier) common.OdigosConfiguration
 		ConfigVersion:             1, // config version starts at 1 and incremented on every config change
 		TelemetryEnabled:          telemetryEnabled,
 		OpenshiftEnabled:          openshiftEnabled,
-		IgnoredNamespaces:         fullIgnoredNamespaces,
+		IgnoredNamespaces:         userInputIgnoredNamespaces,
 		IgnoredContainers:         fullIgnoredContainers,
 		SkipWebhookIssuerCreation: skipWebhookIssuerCreation,
 		Psp:                       psp,
@@ -254,7 +253,7 @@ func init() {
 	installCmd.Flags().StringVar(&autoScalerImage, "autoscaler-image", "keyval/odigos-autoscaler", "autoscaler container image name")
 	installCmd.Flags().StringVar(&imagePrefix, "image-prefix", "", "prefix for all container images. used when your cluster doesn't have access to docker hub")
 	installCmd.Flags().BoolVar(&psp, "psp", false, "enable pod security policy")
-	installCmd.Flags().StringSliceVar(&userInputIgnoredNamespaces, "ignore-namespace", consts.SystemNamespaces, "namespaces not to show in odigos ui")
+	installCmd.Flags().StringSliceVar(&userInputIgnoredNamespaces, "ignore-namespace", consts.DefaultIgnoredNamespaces, "namespaces not to show in odigos ui")
 	installCmd.Flags().StringSliceVar(&userInputIgnoredContainers, "ignore-container", consts.IgnoredContainers, "container names to exclude from instrumentation (useful for sidecar container)")
 	installCmd.Flags().StringSliceVar(&userInputInstallProfiles, "profile", []string{}, "install preset profiles with a specific configuration")
 
diff --git a/cli/cmd/upgrade.go b/cli/cmd/upgrade.go
index 11331a78fb..89df0001b6 100644
--- a/cli/cmd/upgrade.go
+++ b/cli/cmd/upgrade.go
@@ -12,8 +12,6 @@ import (
 	"github.com/odigos-io/odigos/cli/cmd/resources/odigospro"
 	cmdcontext "github.com/odigos-io/odigos/cli/pkg/cmd_context"
 	"github.com/odigos-io/odigos/cli/pkg/confirm"
-	"github.com/odigos-io/odigos/common/consts"
-	"github.com/odigos-io/odigos/common/utils"
 	k8sconsts "github.com/odigos-io/odigos/k8sutils/pkg/consts"
 	"github.com/spf13/cobra"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
@@ -107,9 +105,6 @@ and apply any required migrations and adaptations.`,
 		// update the config on upgrade
 		config.ConfigVersion += 1
 
-		// make sure the current system namespaces is in the ignored in config
-		config.IgnoredNamespaces = utils.MergeDefaultIgnoreWithUserInput(config.IgnoredNamespaces, consts.SystemNamespaces)
-
 		currentTier, err := odigospro.GetCurrentOdigosTier(ctx, client, ns)
 		if err != nil {
 			fmt.Println("Odigos cloud login failed - unable to read the current Odigos tier.")
diff --git a/common/consts/consts.go b/common/consts/consts.go
index 62c6a61521..64e611739f 100644
--- a/common/consts/consts.go
+++ b/common/consts/consts.go
@@ -43,6 +43,6 @@ var (
 )
 
 var (
-	SystemNamespaces  = []string{DefaultOdigosNamespace, "kube-system", "local-path-storage", "istio-system", "linkerd", "kube-node-lease"}
-	IgnoredContainers = []string{"istio-proxy", "vault-agent", "filebeat", "linkerd-proxy", "fluentd", "akeyless-init"}
+	DefaultIgnoredNamespaces = []string{"kube-system", "local-path-storage", "istio-system", "linkerd", "kube-node-lease"}
+	IgnoredContainers        = []string{"istio-proxy", "vault-agent", "filebeat", "linkerd-proxy", "fluentd", "akeyless-init"}
 )
diff --git a/scheduler/controllers/odigosconfig/odigosconfig_controller.go b/scheduler/controllers/odigosconfig/odigosconfig_controller.go
index 69d1507249..5b127ea1df 100644
--- a/scheduler/controllers/odigosconfig/odigosconfig_controller.go
+++ b/scheduler/controllers/odigosconfig/odigosconfig_controller.go
@@ -27,6 +27,10 @@ func (r *odigosConfigController) Reconcile(ctx context.Context, _ ctrl.Request)
 		return ctrl.Result{}, err
 	}
 
+	// make sure the default ignored namespaces are always present
+	odigosConfig.IgnoredNamespaces = mergeIgnoredItemLists(odigosConfig.IgnoredNamespaces, consts.DefaultIgnoredNamespaces)
+	odigosConfig.IgnoredNamespaces = append(odigosConfig.IgnoredNamespaces, env.GetCurrentNamespace())
+
 	err = r.persistEffectiveConfig(ctx, odigosConfig)
 	if err != nil {
 		return ctrl.Result{}, err
diff --git a/scheduler/controllers/odigosconfig/utils.go b/scheduler/controllers/odigosconfig/utils.go
new file mode 100644
index 0000000000..ae45e0222e
--- /dev/null
+++ b/scheduler/controllers/odigosconfig/utils.go
@@ -0,0 +1,20 @@
+package odigosconfig
+
+func mergeIgnoredItemLists(l1 []string, l2 []string) []string {
+
+	merged := map[string]struct{}{}
+
+	for _, i := range l1 {
+		merged[i] = struct{}{}
+	}
+	for _, i := range l2 {
+		merged[i] = struct{}{}
+	}
+
+	mergedList := make([]string, 0, len(merged))
+	for i := range merged {
+		mergedList = append(mergedList, i)
+	}
+
+	return mergedList
+}