yes you can absolutely do that. There are 2-3 Plugins which can deal with multiple identity providers at the same time.
For our own plugin I can absolutely confirm that this can also be 2 different instances of AzureAD.
Our plugin is currently the most installed/most sold on Jira Server & Jira Data-Centre. We also allow you to synchronise your Users & Groups via the Azure Graph API into your Jira if you like to do that.
Here are a couple of links for you:
Also once you setup more than 1 AzureAD (or IdP in general), then you need something that we call "IdP Selection". In the Way the SAML Protocol works, the decision to which AzureAD Tenant to redirect the User to needs to be taken before we know who the User is.
We support a variety of Ways to make this Selection (e.g. IdP Selection Page, Request Headers, Username/E-Mail Domain etc).
A good start if you want to get a reasonable impression before playing around might be to watch the following 2 Videos after each other:
Also if you want to see what other plugins are available in the Marketplace just search for SAML: https://marketplace.atlassian.com/search?product=jira&query=saml
Not all of them support multiple IdPs though and only one other actually support something like User Synchronisation.
P.S. Full disclosure, I work for resolution, a marketplace vendor.
You can have several AD in one jira instance and there is no problem, but as far as i know you only can set one SSO directory (what makes sense). I think you could manage to have SSO for one of the organizations and delegated sign on for the other (meaning jira authenticates against the AD just to give access to those users)
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