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Goto https://portal.azure.com

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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