You can enable backup for Project Online sites from the Office 365 plan page.
Procedure
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From the navigation pane, go to Manage > Plans.
The Plans page appears.
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On the Office 365 tab, in the Plan name column, click a plan for which you want to enable backup for Project Online sites.
The Office 365 plan page appears.
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In the SharePoint pane, move the Backup Project Online toggle key to the right.