diff --git a/.github/workflows/bootstrap.yaml b/.github/workflows/bootstrap.yaml
index b460cd2f..a2572ac4 100644
--- a/.github/workflows/bootstrap.yaml
+++ b/.github/workflows/bootstrap.yaml
@@ -49,7 +49,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITPROVIDER_BOT_TOKEN }}
       - name: uninstall
         run: |
-          ./bin/flux uninstall --resources --crds -s --timeout=10m
+          ./bin/flux uninstall -s --keep-namespace
+          kubectl delete ns flux-system --timeout=10m --wait=true
       - name: bootstrap reinstall
         run: |
           ./bin/flux bootstrap github --manifests ./manifests/install/ \
diff --git a/.github/workflows/e2e.yaml b/.github/workflows/e2e.yaml
index de51ddc1..f1f5b2b4 100644
--- a/.github/workflows/e2e.yaml
+++ b/.github/workflows/e2e.yaml
@@ -195,7 +195,7 @@ jobs:
           ./bin/flux check
       - name: flux uninstall
         run: |
-          ./bin/flux uninstall --crds --silent --timeout=10m
+          ./bin/flux uninstall --silent
       - name: Debug failure
         if: failure()
         run: |
diff --git a/cmd/flux/main.go b/cmd/flux/main.go
index 215a3525..d4410338 100644
--- a/cmd/flux/main.go
+++ b/cmd/flux/main.go
@@ -41,7 +41,7 @@ var rootCmd = &cobra.Command{
 	Example: `  # Check prerequisites
   flux check --pre
 
-  # Install the latest version of the toolkit
+  # Install the latest version of Flux
   flux install --version=master
 
   # Create a source from a public Git repository
@@ -88,8 +88,8 @@ var rootCmd = &cobra.Command{
   # Delete a GitRepository source
   flux delete source git webapp-latest
 
-  # Uninstall the toolkit and delete CRDs
-  flux uninstall --crds
+  # Uninstall Flux and delete CRDs
+  flux uninstall
 `,
 }
 
diff --git a/cmd/flux/uninstall.go b/cmd/flux/uninstall.go
index 8d6027f6..0505d55a 100644
--- a/cmd/flux/uninstall.go
+++ b/cmd/flux/uninstall.go
@@ -22,8 +22,11 @@ import (
 
 	"github.com/manifoldco/promptui"
 	"github.com/spf13/cobra"
-	apierrors "k8s.io/apimachinery/pkg/api/errors"
-	"k8s.io/apimachinery/pkg/types"
+	appsv1 "k8s.io/api/apps/v1"
+	corev1 "k8s.io/api/core/v1"
+	rbacv1 "k8s.io/api/rbac/v1"
+	apiextensionsv1 "k8s.io/apiextensions-apiserver/pkg/apis/apiextensions/v1"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"sigs.k8s.io/controller-runtime/pkg/client"
 
 	"github.com/fluxcd/flux2/internal/utils"
@@ -34,33 +37,27 @@ import (
 
 var uninstallCmd = &cobra.Command{
 	Use:   "uninstall",
-	Short: "Uninstall the toolkit components",
-	Long:  "The uninstall command removes the namespace, cluster roles, cluster role bindings and CRDs from the cluster.",
-	Example: `  # Dry-run uninstall of all components
-  flux uninstall --dry-run --namespace=flux-system
+	Short: "Uninstall Flux and its custom resource definitions",
+	Long:  "The uninstall command removes the Flux components and the toolkit.fluxcd.io resources from the cluster.",
+	Example: `  # Uninstall Flux components, its custom resources and namespace
+  flux uninstall --namespace=flux-system
 
-  # Uninstall all components and delete custom resource definitions
-  flux uninstall --resources --crds --namespace=flux-system
+  # Uninstall Flux but keep the namespace
+  flux uninstall --namespace=infra --keep-namespace=true
 `,
 	RunE: uninstallCmdRun,
 }
 
 type uninstallFlags struct {
-	crds      bool
-	resources bool
-	dryRun    bool
-	silent    bool
+	keepNamespace bool
+	silent        bool
 }
 
 var uninstallArgs uninstallFlags
 
 func init() {
-	uninstallCmd.Flags().BoolVar(&uninstallArgs.resources, "resources", true,
-		"removes custom resources such as Kustomizations, GitRepositories and HelmRepositories")
-	uninstallCmd.Flags().BoolVar(&uninstallArgs.crds, "crds", false,
-		"removes all CRDs previously installed")
-	uninstallCmd.Flags().BoolVar(&uninstallArgs.dryRun, "dry-run", false,
-		"only print the object that would be deleted")
+	uninstallCmd.Flags().BoolVar(&uninstallArgs.keepNamespace, "keep-namespace", false,
+		"skip namespace deletion")
 	uninstallCmd.Flags().BoolVarP(&uninstallArgs.silent, "silent", "s", false,
 		"delete components without asking for confirmation")
 
@@ -68,6 +65,16 @@ func init() {
 }
 
 func uninstallCmdRun(cmd *cobra.Command, args []string) error {
+	if !uninstallArgs.silent {
+		prompt := promptui.Prompt{
+			Label:     "Are you sure you want to delete Flux and its custom resource definitions",
+			IsConfirm: true,
+		}
+		if _, err := prompt.Run(); err != nil {
+			return fmt.Errorf("aborting")
+		}
+	}
+
 	ctx, cancel := context.WithTimeout(context.Background(), rootArgs.timeout)
 	defer cancel()
 
@@ -76,96 +83,189 @@ func uninstallCmdRun(cmd *cobra.Command, args []string) error {
 		return err
 	}
 
-	if !uninstallArgs.dryRun && !uninstallArgs.silent {
-		prompt := promptui.Prompt{
-			Label:     fmt.Sprintf("Are you sure you want to delete the %s namespace", rootArgs.namespace),
-			IsConfirm: true,
-		}
-		if _, err := prompt.Run(); err != nil {
-			return fmt.Errorf("aborting")
-		}
-	}
+	logger.Actionf("deleting components in %s namespace", rootArgs.namespace)
+	uninstallComponents(ctx, kubeClient, rootArgs.namespace)
+
+	logger.Actionf("deleting toolkit.fluxcd.io finalizers in all namespaces")
+	uninstallFinalizers(ctx, kubeClient)
 
-	dryRun := "--dry-run=server"
-	deleteResources := uninstallArgs.resources || uninstallArgs.crds
+	logger.Actionf("deleting toolkit.fluxcd.io custom resource definitions")
+	uninstallCustomResourceDefinitions(ctx, kubeClient, rootArgs.namespace)
 
-	// known kinds with finalizers
-	namespacedKinds := []string{
-		sourcev1.GitRepositoryKind,
-		sourcev1.HelmRepositoryKind,
-		sourcev1.BucketKind,
+	if !uninstallArgs.keepNamespace {
+		uninstallNamespace(ctx, kubeClient, rootArgs.namespace)
 	}
 
-	// suspend bootstrap kustomization to avoid finalizers deadlock
-	kustomizationName := types.NamespacedName{
-		Namespace: rootArgs.namespace,
-		Name:      rootArgs.namespace,
+	logger.Successf("uninstall finished")
+	return nil
+}
+
+func uninstallComponents(ctx context.Context, kubeClient client.Client, namespace string) {
+	selector := client.MatchingLabels{"app.kubernetes.io/instance": namespace}
+	{
+		var list appsv1.DeploymentList
+		if err := kubeClient.List(ctx, &list, client.InNamespace(namespace), selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("Deployment/%s/%s deletion failed: %s", r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("Deployment/%s/%s deleted", r.Namespace, r.Name)
+				}
+			}
+		}
 	}
-	var kustomization kustomizev1.Kustomization
-	err = kubeClient.Get(ctx, kustomizationName, &kustomization)
-	if err == nil {
-		kustomization.Spec.Suspend = true
-		if err := kubeClient.Update(ctx, &kustomization); err != nil {
-			return fmt.Errorf("unable to suspend kustomization '%s': %w", kustomizationName.String(), err)
+	{
+		var list corev1.ServiceList
+		if err := kubeClient.List(ctx, &list, client.InNamespace(namespace), selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("Service/%s/%s deletion failed: %s", r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("Service/%s/%s deleted", r.Namespace, r.Name)
+				}
+			}
 		}
 	}
-	if err == nil || apierrors.IsNotFound(err) {
-		namespacedKinds = append(namespacedKinds, kustomizev1.KustomizationKind)
+	{
+		var list corev1.ServiceAccountList
+		if err := kubeClient.List(ctx, &list, client.InNamespace(namespace), selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("ServiceAccount/%s/%s deletion failed: %s", r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("ServiceAccount/%s/%s deleted", r.Namespace, r.Name)
+				}
+			}
+		}
 	}
-
-	// add HelmRelease kind to deletion list if exists
-	var list helmv2.HelmReleaseList
-	if err := kubeClient.List(ctx, &list, client.InNamespace(rootArgs.namespace)); err == nil {
-		namespacedKinds = append(namespacedKinds, helmv2.HelmReleaseKind)
+	{
+		var list rbacv1.ClusterRoleList
+		if err := kubeClient.List(ctx, &list, selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("ClusterRole/%s deletion failed: %s", r.Name, err.Error())
+				} else {
+					logger.Successf("ClusterRole/%s deleted", r.Name)
+				}
+			}
+		}
 	}
-
-	if deleteResources {
-		logger.Actionf("uninstalling custom resources")
-		for _, kind := range namespacedKinds {
-			if err := deleteAll(ctx, kind, uninstallArgs.dryRun); err != nil {
-				logger.Failuref("kubectl: %s", err.Error())
+	{
+		var list rbacv1.ClusterRoleBindingList
+		if err := kubeClient.List(ctx, &list, selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("ClusterRoleBinding/%s deletion failed: %s", r.Name, err.Error())
+				} else {
+					logger.Successf("ClusterRoleBinding/%s deleted", r.Name)
+				}
 			}
 		}
 	}
+}
 
-	var kinds []string
-	if uninstallArgs.crds {
-		kinds = append(kinds, "crds")
+func uninstallFinalizers(ctx context.Context, kubeClient client.Client) {
+	{
+		var list sourcev1.GitRepositoryList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
+		}
 	}
-
-	kinds = append(kinds, "clusterroles,clusterrolebindings", "namespace")
-
-	logger.Actionf("uninstalling components")
-
-	for _, kind := range kinds {
-		kubectlArgs := []string{
-			"delete", kind,
-			"-l", fmt.Sprintf("app.kubernetes.io/instance=%s", rootArgs.namespace),
-			"--ignore-not-found", "--timeout", rootArgs.timeout.String(),
+	{
+		var list sourcev1.HelmRepositoryList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
+		}
+	}
+	{
+		var list sourcev1.HelmChartList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
+		}
+	}
+	{
+		var list sourcev1.BucketList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
 		}
-		if uninstallArgs.dryRun {
-			kubectlArgs = append(kubectlArgs, dryRun)
+	}
+	{
+		var list kustomizev1.KustomizationList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
 		}
-		if _, err := utils.ExecKubectlCommand(ctx, utils.ModeOS, rootArgs.kubeconfig, rootArgs.kubecontext, kubectlArgs...); err != nil {
-			return fmt.Errorf("uninstall failed: %w", err)
+	}
+	{
+		var list helmv2.HelmReleaseList
+		if err := kubeClient.List(ctx, &list, client.InNamespace("")); err == nil {
+			for _, r := range list.Items {
+				r.Finalizers = []string{}
+				if err := kubeClient.Update(ctx, &r); err != nil {
+					logger.Failuref("%s/%s/%s removing finalizers failed: %s", r.Kind, r.Namespace, r.Name, err.Error())
+				} else {
+					logger.Successf("%s/%s/%s finalizers deleted", r.Kind, r.Namespace, r.Name)
+				}
+			}
 		}
 	}
-
-	logger.Successf("uninstall finished")
-	return nil
 }
 
-func deleteAll(ctx context.Context, kind string, dryRun bool) error {
-	kubectlArgs := []string{
-		"delete", kind, "--ignore-not-found",
-		"--all", "--all-namespaces",
-		"--timeout", rootArgs.timeout.String(),
+func uninstallCustomResourceDefinitions(ctx context.Context, kubeClient client.Client, namespace string) {
+	selector := client.MatchingLabels{"app.kubernetes.io/instance": namespace}
+	{
+		var list apiextensionsv1.CustomResourceDefinitionList
+		if err := kubeClient.List(ctx, &list, selector); err == nil {
+			for _, r := range list.Items {
+				if err := kubeClient.Delete(ctx, &r); err != nil {
+					logger.Failuref("CustomResourceDefinition/%s deletion failed: %s", r.Name, err.Error())
+				} else {
+					logger.Successf("CustomResourceDefinition/%s deleted", r.Name)
+				}
+			}
+		}
 	}
+}
 
-	if dryRun {
-		kubectlArgs = append(kubectlArgs, "--dry-run=server")
+func uninstallNamespace(ctx context.Context, kubeClient client.Client, namespace string) {
+	ns := corev1.Namespace{ObjectMeta: metav1.ObjectMeta{Name: namespace}}
+	if err := kubeClient.Delete(ctx, &ns); err != nil {
+		logger.Failuref("Namespace/%s deletion failed: %s", namespace, err.Error())
+	} else {
+		logger.Successf("Namespace/%s deleted", namespace)
 	}
-
-	_, err := utils.ExecKubectlCommand(ctx, utils.ModeOS, rootArgs.kubeconfig, rootArgs.kubecontext, kubectlArgs...)
-	return err
 }
diff --git a/docs/cmd/flux.md b/docs/cmd/flux.md
index 6686573d..e8642943 100644
--- a/docs/cmd/flux.md
+++ b/docs/cmd/flux.md
@@ -12,7 +12,7 @@ Command line utility for assembling Kubernetes CD pipelines the GitOps way.
   # Check prerequisites
   flux check --pre
 
-  # Install the latest version of the toolkit
+  # Install the latest version of Flux
   flux install --version=master
 
   # Create a source from a public Git repository
@@ -59,8 +59,8 @@ Command line utility for assembling Kubernetes CD pipelines the GitOps way.
   # Delete a GitRepository source
   flux delete source git webapp-latest
 
-  # Uninstall the toolkit and delete CRDs
-  flux uninstall --crds
+  # Uninstall Flux and delete CRDs
+  flux uninstall
 
 ```
 
@@ -88,5 +88,5 @@ Command line utility for assembling Kubernetes CD pipelines the GitOps way.
 * [flux reconcile](flux_reconcile.md)	 - Reconcile sources and resources
 * [flux resume](flux_resume.md)	 - Resume suspended resources
 * [flux suspend](flux_suspend.md)	 - Suspend resources
-* [flux uninstall](flux_uninstall.md)	 - Uninstall the toolkit components
+* [flux uninstall](flux_uninstall.md)	 - Uninstall Flux and its custom resource definitions
 
diff --git a/docs/cmd/flux_uninstall.md b/docs/cmd/flux_uninstall.md
index e0c72bc9..89a383ea 100644
--- a/docs/cmd/flux_uninstall.md
+++ b/docs/cmd/flux_uninstall.md
@@ -1,10 +1,10 @@
 ## flux uninstall
 
-Uninstall the toolkit components
+Uninstall Flux and its custom resource definitions
 
 ### Synopsis
 
-The uninstall command removes the namespace, cluster roles, cluster role bindings and CRDs from the cluster.
+The uninstall command removes the Flux components and the toolkit.fluxcd.io resources from the cluster.
 
 ```
 flux uninstall [flags]
@@ -13,22 +13,20 @@ flux uninstall [flags]
 ### Examples
 
 ```
-  # Dry-run uninstall of all components
-  flux uninstall --dry-run --namespace=flux-system
+  # Uninstall Flux components, its custom resources and namespace
+  flux uninstall --namespace=flux-system
 
-  # Uninstall all components and delete custom resource definitions
-  flux uninstall --resources --crds --namespace=flux-system
+  # Uninstall Flux but keep the namespace
+  flux uninstall --namespace=infra --keep-namespace=true
 
 ```
 
 ### Options
 
 ```
-      --crds        removes all CRDs previously installed
-      --dry-run     only print the object that would be deleted
-  -h, --help        help for uninstall
-      --resources   removes custom resources such as Kustomizations, GitRepositories and HelmRepositories (default true)
-  -s, --silent      delete components without asking for confirmation
+  -h, --help             help for uninstall
+      --keep-namespace   skip namespace deletion
+  -s, --silent           delete components without asking for confirmation
 ```
 
 ### Options inherited from parent commands
diff --git a/docs/guides/installation.md b/docs/guides/installation.md
index 152335f2..5608f19a 100644
--- a/docs/guides/installation.md
+++ b/docs/guides/installation.md
@@ -608,11 +608,27 @@ kustomize build https://github.com/fluxcd/flux2/manifests/install?ref=main | kub
 
 ## Uninstall
 
-You can uninstall the Flux components with:
+You can uninstall Flux with:
 
 ```sh
-flux uninstall --crds
+flux uninstall --namespace=flux-system
 ```
 
-The above command will delete the custom resources definitions, the
-controllers, and the namespace where they were installed.
+The above command performs the following operations:
+
+- deletes Flux components (deployments and services)
+- deletes Flux RBAC (service accounts, cluster roles and cluster role bindings)
+- removes the Kubernetes finalizers from Flux custom resources
+- deletes Flux custom resource definitions and custom resources
+- deletes the namespace where Flux was installed
+
+If you've installed Flux in a namespace that you wish to preserve, you
+can skip the namespace deletion with:
+
+```sh
+flux uninstall --namespace=infra --keep-namespace
+```
+
+!!! hint
+    Note that the `uninstall` command will not remove any Kubernetes objects
+    or Helm releases that were reconciled on the cluster by Flux.
diff --git a/internal/utils/utils.go b/internal/utils/utils.go
index 1113ddda..0acddf35 100644
--- a/internal/utils/utils.go
+++ b/internal/utils/utils.go
@@ -21,7 +21,6 @@ import (
 	"bytes"
 	"context"
 	"fmt"
-	"github.com/fluxcd/flux2/pkg/manifestgen/install"
 	"io"
 	"io/ioutil"
 	"os"
@@ -32,8 +31,10 @@ import (
 	"text/template"
 
 	"github.com/olekukonko/tablewriter"
+	appsv1 "k8s.io/api/apps/v1"
 	corev1 "k8s.io/api/core/v1"
 	rbacv1 "k8s.io/api/rbac/v1"
+	apiextensionsv1 "k8s.io/apiextensions-apiserver/pkg/apis/apiextensions/v1"
 	apiruntime "k8s.io/apimachinery/pkg/runtime"
 	"k8s.io/client-go/rest"
 	"k8s.io/client-go/tools/clientcmd"
@@ -44,6 +45,7 @@ import (
 	kustypes "sigs.k8s.io/kustomize/api/types"
 	"sigs.k8s.io/yaml"
 
+	"github.com/fluxcd/flux2/pkg/manifestgen/install"
 	helmv2 "github.com/fluxcd/helm-controller/api/v2beta1"
 	imageautov1 "github.com/fluxcd/image-automation-controller/api/v1alpha1"
 	imagereflectv1 "github.com/fluxcd/image-reflector-controller/api/v1alpha1"
@@ -163,8 +165,10 @@ func KubeClient(kubeConfigPath string, kubeContext string) (client.Client, error
 	}
 
 	scheme := apiruntime.NewScheme()
+	_ = apiextensionsv1.AddToScheme(scheme)
 	_ = corev1.AddToScheme(scheme)
 	_ = rbacv1.AddToScheme(scheme)
+	_ = appsv1.AddToScheme(scheme)
 	_ = sourcev1.AddToScheme(scheme)
 	_ = kustomizev1.AddToScheme(scheme)
 	_ = helmv2.AddToScheme(scheme)