
Hi Vishakhan,
Normaly when your users with a Microsoft 365 E3 License assigned login to the computer via Entra ID (Entra ID joined device/Intune), the Windows edition should be upgraded automatically.
Here is the right docs on this: https://learn.microsoft.com/en-us/windows/deployment/deploy-enterprise-licenses?pivots=windows-11#assigning-licenses-to-users
Just take note of this:
Windows Enterprise E3 and E5 are available as online services via subscription. Windows Enterprise can be deployed in an organization without keys and reboots.
- Devices with a current Windows Pro edition license can be seamlessly upgraded to Windows Enterprise.
- Product key-based Windows Enterprise software licenses can be transitioned to Windows Enterprise subscriptions.
Organizations that have an enterprise agreement can also benefit from the service, using traditional Active Directory-joined devices. In this scenario, the Active Directory user that signs in on their device must be synchronized with Microsoft Entra ID using Microsoft Entra Connect Sync. So - if you upgrade it via etc. a Windows 11 Pro .iso (available here: https://www.microsoft.com/software-download/windows11) then your users sign in, the edition should be automatically upgraded if meets the above :)
If this is helpfull, place vote or mark as answer.