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Login into Azure and choose Azure Active Directory

Click on Enterprise applications

Click on Add

Click on Non-gallery application

Give Your Application a meaningful name and click on Add

Click Configure single sign-in (required)

Select SAML-based Sign-on as Mode

Fill in the baseUrl of your application as Identifier and the <baseUrl>/plugins/servlet/saml/auth as Reply URL

Here you can also specify the user attributes you want in the SAML Response if you want to create the user

Click on Configure and Click on Endpoints

Click on the copy icon next to Federation Metadata Document to download the IdP XML you need to fill in on the Configure Plugin in the Atlassian Application

Do not forget to change the maxAuthenticationAge

Here is an example how to configure the create User 

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