As the "Embed" web part only allow iframes from whitelisted domains only, we'd like to be able to maintain the list of domains using powershell, instead of manually having to update all of our site manually. I've looked around on internet, but haven't found a way to accomplish this.

Have anyone found a way to get this working on Sharepoint Online (modern sites)?

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Per my knowledge, there is no way for you to edit through PowerShell. You will need to change the settings through UI or allow contributors to insert iframes from any domain.

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