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Inheriting a Messy SharePoint Tenant: A New Admin's Cleanup Guide

Marcus joined Hartley Financial as its first dedicated Microsoft 365 administrator. The previous admin had left six months earlier, and in the gap nobody had actively managed the SharePoint Online environment. On his first day, Marcus pulled up the SharePoint admin centre and found 47 active site collections, no documentation, external sharing enabled at the tenant level, and hundreds of shared links with no expiry dates. He did not know where to start.

This use case follows the three-week process Marcus used to get the tenant under control, using ShareMaster without writing a single line of PowerShell.

What a Neglected SharePoint Tenant Typically Looks Like

Marcus's situation is common. When SharePoint Online grows without a dedicated admin, it usually accumulates the same set of problems:

  • Shared links created by ex-employees that are still active and accessible to anyone with the URL
  • Unique permission overrides scattered across libraries and folders, making the permission model impossible to follow at a glance
  • External users in site collections who no longer work with the organisation
  • Recycling Bins filled with years of deleted content, counting against storage quota
  • Version history growing unchecked, sometimes representing three to five times the volume of live file content
  • No audit record of who changed permissions or when

None of these problems are hard to fix in isolation. The challenge is knowing where they all are across dozens of sites before you can start.

Week 1: Building an Inventory with Report Master

Phase: Understand before acting

Marcus's first priority was a complete picture of the tenant, not action. Acting before understanding the landscape is how things break in a shared environment.

Permission matrix export

He used ShareMaster's Report Master to run its Security Matrix on each of the ten most-used site collections, identified by activity levels in the SharePoint admin centre. Each Excel export came back in a few minutes and showed every user and group with permissions on the site and its lists, libraries and items, their permission level, and where something carried its own permissions instead of inheriting.

Three patterns appeared immediately. Seven accounts belonging to former employees still had Contributor access to client-facing document libraries. Two external guest accounts that had never been removed were still active in the company intranet. One finance library had 34 items with unique permissions breaking the inheritance chain for that folder structure.

Shared links report

The shared links picture was more concerning. Across the ten site collections, ShareMaster's Share Link Finder reports, one workbook per site, found 412 active shared links. The workbooks name each link's type and members but not who created it, so Marcus took that from the Microsoft Purview audit log: 87 links had been created by seven people who had since left the company. Anonymous links, accessible to anyone with the URL regardless of Microsoft 365 account, accounted for 23 of the total.

This kind of visibility is impossible to build from the SharePoint admin centre alone without custom PnP PowerShell scripting. For a step-by-step guide to running this report yourself, see how to audit SharePoint shared links.

Week 2: Fixing the Security Issues First

Note: Address access and sharing risks before touching storage. Cleaning up storage is reversible in the sense that you can restore files from the Recycle Bin; accidentally granting continued access to a former employee's stale shared links is not something you can undo retroactively if it caused a data exposure.

Revoking ex-employee shared links

Share Link Finder does not pick out links by creator: it removes every link in the libraries you choose. Most of the 87 sat in client libraries the leavers had run, where no current link needed to survive, so Marcus cleared each of those libraries with its remove mode (on a Recycle Master or Clone Master licence) in one run. The rest he removed in the browser from each file's Manage access panel. Each revocation removes the link without affecting the underlying file. Any current employee with a legitimate reason to share that content would generate a new link, this time with an expiry date.

Marcus reviewed the 23 anonymous links individually. Nineteen were internal training documents that should never have been shared that way. Four were marketing assets intended to be public but had been shared via anonymous link rather than through the proper public-facing portal. He revoked all 23.

See the Share Link Finder

Removing stale external users and broken inheritance

Marcus removed the two external guest accounts through the Microsoft Entra ID admin centre. For the finance library with 34 unique permission overrides, he used ShareMaster's Explore Master to review the inheritance chain, then used Report Master to confirm what the correct clean state should look like before making changes. Marcus reset the library to inherit from the parent site and replaced the 34 individual overrides with a single Entra ID security group.

For a full walkthrough of the permissions audit process, see how to audit SharePoint Online permissions.

Week 3: Storage Cleanup

Phase: Reclaim quota

With the security work complete, Marcus turned to storage. Report Master's storage export showed the tenant at 71% capacity overall, with three site collections above 85%.

The culprit in two of the three was version history. The sales team's document library had the SharePoint default of 500 major versions per file enabled, and had been active for six years. Version data alone was consuming roughly four times the volume of live file content. Marcus used Space Master's Version Trimmer to set a maximum of 20 major versions per file and ran the trim across the three heavy libraries. Storage in those libraries dropped by more than 60%.

The Recycling Bin across all ten site collections held 8.3 GB of deleted content, items accumulated over six years with no systematic clearing. Recycle Master reads one site collection's bin at a time, so Marcus spot-checked the three largest sorted by deletion date, confirmed there was nothing worth restoring, and then ticked all ten in the bulk clear and emptied both stages in a single operation.

Three Weeks Later: What Changed

Issue Before After
Active links created by ex-employees 87 0
Anonymous shared links 23 0
Stale external guest accounts 2 0
Tenant storage utilisation 71% 44%
Site collections above 85% capacity 3 0
Documented permission model None Excel export for each site collection

Marcus now runs a Report Master permission export monthly and reviews shared links quarterly. The first time he ran these, they were remediation projects spanning weeks. Now each takes about 20 minutes.

Frequently Asked Questions

How long does a full SharePoint tenant permissions audit take?

With manual SharePoint admin centre reports, a full audit across 50 or more sites can take several days. ShareMaster's Report Master generates a permission matrix export for an entire site collection in a few minutes, reducing the discovery phase from days to hours.

Can I see who created a shared link in SharePoint Online?

Yes, from the Microsoft Purview audit log, which records sharing events with the user and date. Neither SharePoint's site sharing report nor ShareMaster's Share Link Finder shows who created a link or when. Share Link Finder reports each link's type and members in the libraries you pick on a site and, on a Recycle Master or Clone Master licence, removes all links in those libraries in one run.

Is it safe to bulk-revoke shared links in SharePoint Online?

Yes. Revoking a shared link removes access for anyone using that link but does not delete or alter the underlying file. If a legitimate user was relying on the link, they would need to request a new one. For links created by former employees or with no expiry date, revocation is generally the right action.

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