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Getting error below, tried to setup for the first time last night and I think I stuffed up something.
AADSTS700016: Application with identifier 'https://auth.atlassian.com/saml/21466960-f66a-48ab-8b65-59ba9dd03432' was not found in the directory '1b7e008e-8d66-427b-9e8a-a91aa2d75bcb'. This can happen if the application has not been installed by the administrator of the tenant or consented to by any user in the tenant. You may have sent your authentication request to the wrong tenant.
I can't login to create a support ticket, anyone able to assist.
Atlassian recommend to have an org admin user account other than the domain account to recover such issues if any thing goes wrong with SSO.
What happens in your case is the directory id is wrong on Azure Side , please update the Atlassian url with correct directory id on Azure SSO configuration .
Update Azure with this url "'https://auth.atlassian.com/saml/21466960-f66a-48ab-8b65-59ba9dd03432"
On Azure side , if you have two applications delete one of them and update the right directory id on the other one
Then the only way is, please create the support ticket to atlassian and request them to disable the SSO on your instance.