is there a way to disable programmatic access for users Signing in using AWS SSO? Is it possible to control the programmatic and console access using polices or Groups?
Disable programatic access for AWS SSO user
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The permissions a user has through SSO can still be managed through AWS IAM (Identity and Access Management) groups and rols. The same permissions a user has through IAM in the AWS console can be used by the user when accessing AWS programatically throught the CLI or an SDK.
No permissions are required for a user to get a session token. The purpose of the GetSessionToken operation is to authenticate the user using MFA. You cannot use policies to control authentication operations. Source
Therefore, I don't think that you can prevent a user from using access keys to get temporary session tokes for programmatic access.
Why do you want to prevent programmatic access for users and am I right assuming that you mean CLI and SDK access to AWS by programmatic access?
Yes, you can, but exactly how will be buried in the implementation details of your organization's SSO implementation. Your SSO's custom identity broker is in charge of mapping a particular user's AD credentials to an AWS IAM role, which may or may not have permissions to login to the CLI. Exactly which role a user gets needs to be controllable in the broker. Another way is to control access to the AWS access keys needed to use the CLI or SDKs. Your SSO users shouldn't have permission to generate their own keys. They should come from IT or should be a configurable feature of your SSO implementation. For example, in my organization, there are 2 links in the AWS portal; one for console access and one to display temporary access keys that can be copied into the bash environment or used with an SDK.