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Implemented a custom SAML identity provider which is providing SAML claim in below format i:0e.t|SAML provider|domain\user while Window authentication is accepting in i:0#.w|domain\user format, leading to two parallel identities for same user and creating new claim type for already existing user.

Please note we are pulling user data from same LDAP for both identity provider.

How can we encode this identity either at custom SAML identity provider or SharePoint side (using custom code) which lets us handle the claim based tokens and authorize the users using their Windows account?

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If the same windows user can access via ADFS, you should consider to migrate your windows users to adfs using the powershell command. Move-SPUser This will take care of all user permissions as well.
Source : https://blogs.msdn.microsoft.com/sambetts/2014/09/03/how-to-migrate-sharepoint-users-to-adfs/

  • Hello Kushal...thanks for the reply but we are trying to avoid any kind of migration of the users as you mentioned above. Is there any way of doing the same using custom code? – Tarun K Dec 14 '16 at 10:45

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