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I am using a SPFX Script Editor to make color changes on the Header of the Home Page. Now, when I visit other pages in the SharePoint site like-Site Contents, I don't see the changes applied to the header.

How can I ensure that the changes are applied across the site? Is it possible to edit the master page on the Communication site?

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That is not possible and the script editor is only modifying the page on which the webpart is installed. There might be a way, though i have not tested it.

Try and look for SPFX Extensions and see if they allow "global deployment". If that does not work, then there is no way to globally edit styles.

https://docs.microsoft.com/en-us/sharepoint/dev/spfx/extensions/overview-extensions

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This is by design. As Dante.R mentioned, the Script Editor web part is only modifying the page on which the webpart is added.

Per my knowledge, currently, customizing master page is not supported on the Communication site.

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