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I need to take an entire subsite on our company's intranet (SharePoint 2013 Enterprise) and copy it to our parent company's intranet (SharePoint Online/365). The two sites are completely different farms, webapps, etc. The site I'm trying to copy is not its own site collection - it's two levels down from the site collection root.

I have limited access to the 365 environment, so using a solution file or Powershell is out. I am a site collection admin on both sites. For some reason, I don't seem to have the "Save as site template" option under the site's settings, which was the solution I found after searching, but that is a separate issue I may have to fix provided the template will cross versions as needed.

How can a site admin copy/clone a subsite from a 2013 on-site webapp to a 365 one?

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As per your requirement, you can move the site from onprem to cloud using 3rd party tools. There is no other way, like using PowerShell, admin center recover etc.check sharegate or metalogix etc.

You can also try to move the content manually from onprem to cloud.

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If you have publishing feature enabled in your site, you may face issue for saving the site as template. Please see below link to enable it:

http://www.learningsharepoint.com/2013/05/03/missing-save-site-as-template-for-publishing-sites-in-sharepoint-2013/

The other approach is to use third party tool like metalogics or Sharegate.

If you have only list and libraries to migrate, then you can create stp of it and add them to O365 directly. But if you have more things to migrate like workflow, pages and style library, then go with third party tool for migration.

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