You can manually remove individual sites from SharePoint Online backup content using the Exclude Content tool. When you exclude a site, backup jobs no longer run on that site.
Procedure
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From the navigation pane, go to Protect > Office 365.
The Office 365 Overview page appears.
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On the Apps tab, click the app.
The Overview page of the app appears.
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On the Content tab, in the upper-right area of the page click Add.
The Configure Content page appears.
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Select Exclude content from backup, and then click Next.
The Exclude Content tool appears.
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Under Standard, select Sites, and then click Next.
The Content tab appears.
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In the list, select the sites that you want to exclude from backups, and then click Next.
The Summary tab appears.
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Click Submit.