You’ll probably want to start with the SharePoint Online Management Shell:

Install-Module -Name Microsoft.Online.SharePoint.PowerShell

Once that’s installed, you can use it to pull a list of sites along with useful metadata like URL, owner, storage usage, and last content modification date:

Get-SPOSite | Select Url, Owner, StorageUsageCurrent, LastContentModifiedDate

That gives you enough to start filtering things down. For example, you can narrow it to sites under 1 GB that haven’t been modified since 2024.

Get-SPOSite | Where-Object {

$_.StorageUsageCurrent -lt 1024 -and

$_.LastContentModifiedDate -lt (Get-Date "2024-01-01")

}

Before doing anything destructive, you’ll likely want to add yourself as a site collection admin so you have full access:

Set-SPOUser -Site -LoginName your@domain.com -IsSiteCollectionAdmin $true

And once you’re confident in your filtering, you can remove sites with:

Remove-SPOSite -Identity

That handles most of the site-level cleanup pretty cleanly.

The folder cleanup is where things gets harder. The SharePoint Online module is really geared toward tenant and site administration, not walking through document libraries. If you need to safely delete folders based on modification dates, you can’t just rely on the folder’s own timestamp. You have to look at everything inside it and make sure nothing has been modified more recently. For that part, you’ll probably want to use Microsoft Graph or PnP PowerShell so you can recurse through the structure properly.