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Flux and SOPS on AKS with workload identity

· 8 min read

Setting up sops with flux and workload identity on AKS is not a complex procedure however there is a lack of proper documentation for some steps.

I was working on setting this up on Azure Kubernetes Service and getting stuck at the point where I had to actually decrypt a secret from a sample deployment.

The key point to understand is that the application responsible for decrypting the secrets is the kustomize-controller. We aim then to have a managed identity assigned to the service-account of the kustomize-controller deployed by flux and to enable workload identity on both the service account and the pods. This requires some azure specific labels and annotations to be added to the k8s resources.

I aim to provide a recap on how to deploy all of this with links to the relevant documentation and add the sample yaml needed to assign and use the identity.

We aim to have:

  • An AKS cluster deployed with workload identity enabled
  • A managed identity with a federated credential
  • A key vault to store the encryption key, an encryption key and access policy to allow the managed identity to encrypt using the key
  • A github repo to be our source of truth for k8s deployment
  • Flux deployed in the cluster
  • Flux resources patched to enable workload identity
  • A sample encrypted secret in the repo

If you just want to check the end result this is the repo with all the files.

Please note that there some values in the files and scripts that needs to be updated according to your environment, such as resource group name or reference to github repo.

Required tooling on workstation

We will use:

  • az CLI
  • Flux CLI
  • sops CLI

In addition to that but not strictly required:

  • vs code with bicep extension for code editing
  • kubectl for troubleshooting/inspection of k8s cluster

I'll perform the deployment from a devcontainer based on debian with all the tools required already installed but of course this is doable from any Windows/Linux machine and from WSL within Windows.

I will add some description for all the steps below and I will provide a repo with all the scripts and yaml files organized into two folders:

  • iac
  • gitops

A better approach would be to have two github repos, one for infrastructure, one for k8s deployment. However I want to keep things manageable for this post and I'll use just one repo. I structured the azure resources in 3 modules, described below. A main.bicep file put everything together.

AKS with workload identity enabled - aks.bicep

There are several options to deploy a workload enabled cluster on Azure. My preferred option is to go with bicep, since it has decent tooling and it is idempotent by default.

Regardless of the deployment method, we need to enable workload identity and get the OIDC issuer URL for the cluster to be used in a subsequent step.

The OIDC Issuer URL is required to set up the federated credentials on the managed identity that's why we have it as an output.

This is my sample deployment.

param location string

resource aks 'Microsoft.ContainerService/managedClusters@2023-08-01' = {
name: 'my-aks'
location: location
identity: {
type: 'SystemAssigned'
sku: {
name: 'Base'
tier: 'Free'
properties: {
kubernetesVersion: '1.26.6'
agentPoolProfiles: [
name: 'system'
mode: 'System'
vmSize: 'Standard_B2ms'
count: 1
enableAutoScaling: false
osType: 'Linux'
osSKU: 'AzureLinux'
dnsPrefix: 'my-aks-dns'
oidcIssuerProfile: {
enabled: true
securityProfile: {
workloadIdentity: {
enabled: true
networkProfile: {
loadBalancerSku: 'basic'

output oidcIssuerURL string =

Managed identity - mi.bicep

The managed identity is going to be used by the kustomize-controller to get access to the encryption key. The service account of the kustomize-controller has an account token that is going to be exchanged with an azure ad token that will permit access to the key-vault.

We will use the principal id to allow the managed identity to access the encryption key.

param location string

param aksIssuerURL string

resource managedIdentity 'Microsoft.ManagedIdentity/userAssignedIdentities@2023-01-31' = {
name: 'kustomize-controller-mi'
location: location

// we need to federate aks with azure ad
resource federatedCredentials 'Microsoft.ManagedIdentity/userAssignedIdentities/federatedIdentityCredentials@2023-01-31' = {
name: 'aks-fc'
parent: managedIdentity
properties: {
audiences: [
issuer: aksIssuerURL
subject: 'system:serviceaccount:flux-system:kustomize-controller'

output objectId string =

KeyVault - kv.bicep

Deploy a key vault with bicep, adding an encryption key and relevant access policies.

param location string

param managedIdentityObjectId string

resource keyVault 'Microsoft.KeyVault/vaults@2023-02-01' = {
name: 'my-kv-${uniqueString(resourceGroup().id)}'
location: location
properties: {
sku: {
family: 'A'
name: 'standard'
tenantId: tenant().tenantId
accessPolicies: [
objectId: managedIdentityObjectId
tenantId: tenant().tenantId
permissions: {
keys: [

resource key 'Microsoft.KeyVault/vaults/keys@2023-02-01' = {
name: 'encryption-key'
parent: keyVault
properties: {
attributes: {
enabled: true
exportable: false
kty: 'RSA'
keySize: 2048

Github repo

We will use this repo to bootstrap Flux, you want to have a dedicated repo but as I said before I'll keep all the code from the blog post in a single repo, including infrastructure as code part.

Bootstrap flux

In the gitops folder of the repo, the script I used to setup flux. Please note that the inner aks folder was empty when I ran the script.

Please update the script to refer to your github account or check Flux documentation for additional providers.

If you will use GitHub then you will be prompted for a personal access token, create one with repo access. A short expiration date is fine, Flux will add a deploy key to the repo to access it in the future.

When the command is complete the aks folder is populated with a flux-system sub-folder.

Patch flux

Now we have to "assign" the managed identity to the service account and to enable workload identity. This is the step for which I couldn't find any documentation.

To do that we will patch two resources created by Flux. I like to organize patches into a subfolder patches and have one file per resource.

Expected structure is:

  • gitops:
    • aks:
      • flux-system:
        • gotk-components.yaml
        • gotk-sync.yaml
        • kustomization.yaml [TO MODIFY]
        • patches:
          • kustomize-controller-deployment.yaml [NEW]
          • kustomize-controller-service-account.yaml [NEW]

The kustomization.yaml files has to be updated to

kind: Kustomization
- gotk-components.yaml
- gotk-sync.yaml

- path: patches/kustomize-controller-deployment.yaml
- path: patches/kustomize-controller-service-account.yaml

The kustomize-controller-deployment.yaml can be copied as it is, while for the kustomize-controller-service-account.yaml you will need to retrieve client id and tenant id for the deployed managed identity.

You can use the following command, possibly updating the value of the resource group name.

az identity list -g flux-workload-identity-post

Update the yaml with the relevant values

apiVersion: v1
kind: ServiceAccount
name: kustomize-controller
namespace: flux-system
azure.workload.identity/client-id: <your value>
azure.workload.identity/tenant-id: <your value>
azure.workload.identity/use: "true"

Now commit all the changes and push. It will take a few minutes to complete the deployment. You can check the status using:

flux get all -A

Add a sample secret

Let's see the result from a file-system point of view, please setup files and folder as shown below. My repo has this final setup. Having a structure exactly like this one is probably not required, I'm not an expert on flux nor gitops, feel free to adjust to your needs.

  • gitops:
    • aks:
      • kustomization.yaml [NEW]
      • apps.yaml [NEW]
      • apps:
        • kustomization.yaml [NEW]
        • namespace.yaml [NEW]
        • secret.yaml [NEW]
      • flux-system:
        • gotk-components.yaml
        • gotk-sync.yaml
        • kustomization.yaml
        • patches:
          • kustomize-controller-deployment.yaml
          • kustomize-controller-service-account.yaml

You can copy the content of all files except for secret.yaml and possibly apps.yaml. Let's start with the latter:

kind: Kustomization
name: apps
namespace: flux-system
- name: flux-system
interval: 2m0s
kind: GitRepository
name: flux-system
path: ./gitops/aks/apps # if your folder structure is different change this path to reflect where you want to deploy the secret
prune: true
wait: true
timeout: 5m0s
provider: sops # here we are telling flux that we are using sops

For the secret, mine is already encrypted but we have to start with a clear text one

apiVersion: v1
kind: Secret
name: sample-secret
namespace: sops-workload-identity
type: Opaque
sops_encrypted_secret: value of the secret

With the following command

sops -e -i --encrypted-regex '^(data|stringData)$' --azure-kv [url to the encryption key] secret.yaml

This will encrypt only the stringData part, however all the file content is added to the checksum so it cannot be changed outside of sops. From now on, to edit the secret run sops secret.yaml.

Now commit and push. After the deployment is completed, your cluster should have access to the secret:

kubectl get secret sample-secret -n sops-workload-identity -o jsonpath='{.data.*}' | base64 -d