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Showing content from https://docs.github.com/en/enterprise-cloud@latest/apps/using-github-apps/saml-and-github-apps below:

SAML and GitHub Apps - GitHub Enterprise Cloud Docs

If your organization or enterprise is SSO protected, you may need to start an active SSO session for your organization before authorizing, installing, or requesting a GitHub App.

If your organization or enterprise uses SSO, you may not be able to see your organization's resources or enterprise's internal resources after you authorize a GitHub App. For example, if the app displays a list of repositories, you may not see repositories owned by your organization. To resolve this issue, follow these steps:

1. Go to https://github.com/orgs/ORGANIZATION-NAME/sso to start an active SAML session for your organization. Replace ORGANIZATION-NAME with the name of your organization.
   • If your enterprise manages SSO for your organization, you can also go to https://github.com/enterprises/ENTERPRISE-NAME/sso to start an active SSO session for your enterprise. Replace ENTERPRISE-NAME with the name of your enterprise. This works as an SSO session for all organizations in the enterprise that you're a member of.
   • Attempting to access any resources owned by the account will also trigger SSO if you don't have a session already.
2. Revoke your authorization of the GitHub App. For more information, see Reviewing and revoking authorization of GitHub Apps.
3. Reauthorize the GitHub App. GitHub App authorization is initiated by the app and varies based on the app. For example, some GitHub Apps may have you click on a link or enter a command in your terminal. For more information, see Authorizing GitHub Apps.

When you sign in to an app, a credential authorization is created for each organization that you have an SSO session for. SSO can be enforced at the organization or enterprise level. If it's enforced at the enterprise level, having an SSO session with any organization counts as an SSO session for each organization you're a member of. This will appear as a credential authorization on the token for each organization you are a member of at the time of the application authorization.

The SSO credential authorization is tied to the specific sign-in session with the app. If you plan to sign in to the app again on another device or after your SSO sessions expire, you will need to start new SSO sessions before you sign in to ensure the app can access your organization's resources.

If your organization or enterprise uses SSO, you may not see your organization listed when you try to install or request an GitHub App for your organization. To resolve this issue, follow these steps:

1. Go to https://github.com/orgs/ORGANIZATION-NAME/sso to start an active SAML session for your organization. Replace ORGANIZATION-NAME with the name of your organization.
   • If your enterprise manages SSO for your organization, you can also go to https://github.com/enterprises/ENTERPRISE-NAME/sso to start an active SSO session for your enterprise. Replace ENTERPRISE-NAME with the name of your enterprise. This works as an SSO session for all organizations in the enterprise that you're a member of.
2. Try to install or request the GitHub App again. For more information, see Installing a GitHub App from a third party, Installing a GitHub App from GitHub Marketplace for your organizations, and Requesting a GitHub App from your organization owner.

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