diff --git a/README.md b/README.md
index 769baf1..cfbcfa2 100644
--- a/README.md
+++ b/README.md
@@ -17,8 +17,9 @@ the lifecycle of CNCF [Flux CD](https://fluxcd.io) and the
 
 ## Features
 
-- Provide a declarative API for the installation and upgrade of the Flux distribution.
+- Provide a declarative API for the installation, sync configuration and upgrade of the Flux distribution.
 - Automate patching for hotfixes and CVEs affecting the Flux controllers container images.
+- Support for syncing the custer state from Git repositories, OCI artifacts and S3-compatible storage.
 - Provide first-class support for OpenShift, Azure, AWS, GCP and other marketplaces.
 - Simplify the configuration of multi-tenancy lockdown on shared Kubernetes clusters.
 - Provide a security-first approach to the Flux deployment and FIPS compliance.
@@ -144,14 +145,58 @@ kubectl create secret docker-registry flux-enterprise-auth \
   --docker-password=$ENTERPRISE_TOKEN
 ```
 
-### Migration of a bootstrap cluster
+### Cluster Sync
+
+The `FluxInstance` resource can be configured to instruct the operator to generate 
+a Flux source (`GitRepository`, `OCIRepository` or `Bucket`) and a Flux `Kustomization`
+to sync the cluster state with the source repository.
+
+The Flux objects are created in the same namespace where the `FluxInstance` is deployed
+using the namespace name as the Flux source and Kustomization name. The naming convention
+matches the one used by `flux bootstrap` to ensure compatibility with upstream, and
+to allow [transitioning](#migration-of-a-bootstrapped-cluster)
+a bootstrapped cluster to a `FluxInstance` managed one.
+
+To sync the cluster state from a Git repository, add the following configuration to the `FluxInstance`:
+
+```yaml
+apiVersion: fluxcd.controlplane.io/v1
+kind: FluxInstance
+metadata:
+  name: flux
+  namespace: flux-system
+spec:
+  sync:
+    kind: GitRepository
+    url: "https://github.com/my-org/my-fleet.git"
+    ref: "refs/heads/main"
+    path: "clusters/my-cluster"
+    pullSecret: "flux-system"
+```
+
+If the source repository is private, the Kubernetes secret must be created in the `flux-system` namespace
+and should contain the credentials to clone the repository:
+
+```shell
+flux create secret git flux-system \
+  --url=https://github.com/my-org/my-fleet.git \
+  --username=git \
+  --password=$GITHUB_TOKEN
+```
+
+> [!NOTE]
+> For more information on how to configure the cluster sync, refer to the
+> [FluxInstance API documentation](https://github.com/controlplaneio-fluxcd/flux-operator/blob/main/docs/api/v1/fluxinstance.md#sync-configuration).
+
+### Migration of a bootstrapped cluster
 
 To migrate a cluster that was bootstrapped, after the flux-operator is installed
-and the `FluxInstance` resource is created, the following steps are required:
+and the `FluxInstance` resource is created with a [sync source](#cluster-sync),
+the following steps can be followed:
 
 1. Checkout the branch of the Flux repository that was used to bootstrap the cluster.
-2. Replace the contents of the `flux-system/gok-components.yaml` with the `FluxInstance` YAML manifest.
-3. Remove all controllers patches from the `flux-system/kustomization.yaml`.
+2. Delete the `flux-system` directory from the repository `clusters/my-cluster` directory.
+3. Optionally, place the `FluxInstance` YAML manifest in the `clusters/my-cluster` directory.
 4. Commit and push the changes to the Flux repository.
 
 ## Supply Chain Security
diff --git a/docs/api/v1/fluxinstance.md b/docs/api/v1/fluxinstance.md
index 5ee2322..ca81729 100644
--- a/docs/api/v1/fluxinstance.md
+++ b/docs/api/v1/fluxinstance.md
@@ -329,6 +329,174 @@ The reconciliation behaviour can be configured using the following annotations:
 - `fluxcd.controlplane.io/reconcileEvery`: Set the reconciliation interval. Default is `1h`.
 - `fluxcd.controlplane.io/reconcileTimeout`: Set the reconciliation timeout. Default is `5m`.
 
+### Sync configuration
+
+The `.spec.sync` field is optional and specifies the Flux sync configuration.
+When set, a Flux source and a Flux Kustomization are generated to sync
+the cluster state with the source repository.
+
+The Flux objects are created in the same namespace where the FluxInstance is deployed
+using the namespace name as the Flux source and Kustomization name. The naming convention
+matches the one used by `flux bootstrap` to ensure compatibility with upstream, and
+to allow transitioning a bootstrapped cluster to a FluxInstance managed one.
+
+Sync fields:
+
+- `kind`: The source kind, supported values are `GitRepository`, `OCIRepository` and `Bucket`.
+- `url`: The URL of the source repository, can be a Git repository HTTP/S or SSH address, an OCI repository address or a Bucket endpoint.
+- `ref`: The source reference, can be a Git ref name e.g. `refs/heads/main`, an OCI tag e.g. `latest` or a Bucket name.
+- `path`: The path to the source directory containing the kustomize overlay or plain Kubernetes manifests to sync from.
+- `pullSecret`: The name of the Kubernetes secret that contains the credentials to pull the source repository. This field is optional.
+- `interval`: The sync interval. This field is optional, when not set the default is `1m`.
+
+### Sync from Git over HTTP/S
+
+Example:
+
+```yaml
+spec:
+  sync:
+    kind: GitRepository
+    url: "https://gitlab.com/my-group/my-fleet.git"
+    ref: "refs/heads/main"
+    path: "clusters/my-cluster"
+    pullSecret: "git-token-auth"
+```
+
+If the source repository is private, the Kubernetes secret must be created
+in the same namespace where the FluxInstance is deployed, and have the following format:
+
+```yaml
+apiVersion: v1
+kind: Secret
+metadata:
+  name: git-token-auth
+  namespace: flux-system
+type: Opaque
+stringData:
+  username: "git-username"
+  password: "git-token"
+```
+
+To generate the secret with the Flux CLI:
+
+```sh
+flux create secret git git-token-auth \
+  --namespace flux-system \
+  --url=https://gitlab.com/my-group/my-fleet.git \
+  --username=git-username \
+  --password=git-token
+```
+
+### Sync from Git over SSH
+
+Example:
+
+```yaml
+spec:
+  sync:
+    kind: GitRepository
+    url: "ssh://git@github.com/my-org/my-fleet.git"
+    ref: "refs/heads/main"
+    path: "clusters/my-cluster"
+    pullSecret: "git-ssh-auth"
+```
+
+If the source repository is private, the Kubernetes secret must be created
+in the same namespace where the FluxInstance is deployed, and have the following format:
+
+```yaml
+apiVersion: v1
+kind: Secret
+metadata:
+  name: git-ssh-auth
+  namespace: flux-system
+type: Opaque
+stringData:
+  identity: |
+    -----BEGIN OPENSSH PRIVATE KEY-----
+    ...
+    -----END OPENSSH PRIVATE KEY-----    
+  known_hosts: |
+    github.com ecdsa-sha2-nistp256 AAAA...  
+```
+
+To generate the secret with the Flux CLI:
+
+```sh
+flux create secret git git-ssh-auth \
+  --namespace flux-system \
+  --url=ssh://git@github.com/my-org/my-fleet.git \
+  --private-key-file=my-private.key
+```
+
+### Sync from OCI over HTTP/S
+
+Example:
+
+```yaml
+spec:
+  sync:
+    kind: OCIRepository
+    url: "oci://ghcr.io/my-org/my-fleet-manifests"
+    ref: "latest"
+    path: "clusters/my-cluster"
+    pullSecret: "oci-token-auth"
+```
+
+If the container registry is private, the Kubernetes secret must be created
+in the same namespace where the FluxInstance is deployed, and be of type `kubernetes.io/dockerconfigjson`:
+
+```yaml
+apiVersion: v1
+kind: Secret
+metadata:
+  name: oci-token-auth
+  namespace: flux-system
+type: kubernetes.io/dockerconfigjson
+data:
+  .dockerconfigjson: "base64-encoded-docker-config"
+```
+
+To generate the secret with the Flux CLI:
+
+```sh
+flux create secret oci oci-token-auth \
+  --namespace flux-system \
+  --url=ghcr.io \
+  --username=ghcr-username \
+  --password=ghcr-token
+```
+
+### Sync from S3-compatible storage over HTTP/S
+
+Example:
+
+```yaml
+spec:
+  sync:
+    kind: Bucket
+    url: "minio.my-org.com"
+    ref: "my-bucket-fleet"
+    path: "clusters/my-cluster"
+    pullSecret: "bucket-auth"
+```
+
+If the Bucket is private, the Kubernetes secret must be created
+in the same namespace where the FluxInstance is deployed, and have the following format:
+
+```yaml
+apiVersion: v1
+kind: Secret
+metadata:
+  name: bucket-auth
+  namespace: flux-system
+type: Opaque
+stringData:
+  accesskey: "my-accesskey"
+  secretkey: "my-secretkey"
+```
+
 ## FluxInstance Status
 
 ### Conditions
diff --git a/internal/controller/fluxinstance_controller_test.go b/internal/controller/fluxinstance_controller_test.go
index 5bdf556..84a3685 100644
--- a/internal/controller/fluxinstance_controller_test.go
+++ b/internal/controller/fluxinstance_controller_test.go
@@ -476,6 +476,7 @@ func TestFluxInstanceReconciler_Profiles(t *testing.T) {
 	sync.SetAPIVersion("kustomize.toolkit.fluxcd.io/v1")
 	sync.SetKind("Kustomization")
 	err = testClient.Get(ctx, types.NamespacedName{Name: ns.Name, Namespace: ns.Name}, &sync)
+	g.Expect(err).ToNot(HaveOccurred())
 
 	// Check multitenant profile.
 	nestedString, b, err := unstructured.NestedString(sync.Object, "spec", "serviceAccountName")