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One of our users requires a column in their Document Library to enforce unique values, however the library contains more documents than the 5000 item threshold limit.

Whenever you try to switch on the setting you are met with an error:

"Sorry, something went wrong The attempted operation is prohibited because it exceeds the list view threshold enforced by the administrator"

Are there any other ways to change this setting?

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It is not suggested to have more than 5000 item in a library.

Manage large lists and libraries in SharePoint for your reference:

https://support.office.com/en-us/article/manage-large-lists-and-libraries-in-sharepoint-b8588dae-9387-48c2-9248-c24122f07c59#ID0EAABAAA=Online

You can try to use PowerShell to Make a column unique in SharePoint Online.

SharePoint Online: change list field settings using PowerShell for your reference:

https://www.sharepointdiary.com/2017/07/sharepoint-online-set-list-field-settings-using-powershell.html

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