My current setup is ECS when every task have it’s own AWS IAM role, configured in Atlas as IAM role with relevant access.
Now we move to EKS, but I’m not sure how I can provide access? The only thing I found is creating IAM user, and generate keys, and use them in the pod. But this is too messy.
What is the right way to make the access easily and bind between service account to atlas access?

7 months later

I think you should be able to use EKS pod identity. Like this your pod will be able to assume IAM role and like ECS you are supposed to use this role to access the MongoDB Atlas cluster.
Hope this helps if so let us know.
Thank you!