Back up folders that live outside OneDrive: the junction-link trick that just works

TL;DR. OneDrive only syncs files that live inside its own folder. If you have project data, scanned documents, archives, or QuickBooks files in D:\, C:\Customers, or anywhere else, OneDrive ignores them by default — and they are not backed up. The fix is a one-line Windows command that creates a junction: a special pointer inside your OneDrive folder that the sync engine follows out to the real location. The files stay where they are, OneDrive sees them anyway, and they get uploaded to your tenant.

Why this comes up

The default OneDrive setup — including the “Known Folder Move” option — protects exactly three folders: Desktop, Documents, and Pictures. Anything else is on you. Common things our clients want backed up that fall outside that scope:

• QuickBooks company files (often on a D:\Quickbooks drive)
• Customer or project folders on a secondary drive
• Saved CAD, video, or design files in dedicated workspace folders
• Scan-to-folder targets used by office multi-function copiers
• Old archived data the user does not want to physically relocate

You could move those folders inside OneDrive — but you usually do not want to. Existing apps may have hard-coded paths, the data might be huge, or the folder may be shared with another machine on the LAN. The junction approach lets you leave everything where it is and still get OneDrive backup.

How junctions work (briefly)

NTFS supports special filesystem objects called junctions (and symbolic links) that look like a folder but are actually a pointer to a different folder somewhere else on the system. When OneDrive’s sync engine traverses your OneDrive folder and hits a junction, it follows the pointer and uploads whatever it finds there — just as if the files were really inside OneDrive.

The key facts about junctions:

• They look and behave like a regular folder to apps and File Explorer.
• The real files are not duplicated — they live in their original location.
• A junction is bidirectional: changes saved through the junction or through the original path show up in both places, because they are literally the same files.
• OneDrive will sync the contents to the cloud and to any other devices linked to the same OneDrive account — on those other devices the files appear inside OneDrive normally.
• Junctions only work on the same machine across local NTFS volumes. They do not work across UNC paths or to network drives. (For network shares, see “What about network drives?” below.)

The exact command

Open Command Prompt as Administrator and run:

mklink /J "C:\Users\YourName\OneDrive\BackupLink-Customers" "D:\Customers"

Substitute the obvious bits:

• YourName — your Windows user account folder.
• If your OneDrive is the business / Microsoft 365 version, the path will look like OneDrive - InfiNet Computer Solutions, Inc. instead of just OneDrive.
• BackupLink-Customers — the name that will appear inside OneDrive. We like to prefix junction names with BackupLink- so that two years from now you remember why that folder is there.
• D:\Customers — the real folder you want backed up.

That is it. Within a few seconds OneDrive notices the new “folder,” starts uploading, and a green check mark appears on the junction once everything is synced.

Verifying it worked

1. Open File Explorer and navigate to your OneDrive folder. You should see BackupLink-Customers with a slightly different folder icon (an arrow / shortcut overlay).
2. Open it. You should see exactly the same contents as D:\Customers.
3. Wait a few minutes (or longer if the folder is large). The OneDrive cloud icon in your system tray will tell you when it has finished syncing.
4. Log into OneDrive on the web. The folder should be visible there and you should be able to download a file from it. That is your confirmation it is in the cloud.

What to watch out for

• Files On-Demand can save space. Once OneDrive has uploaded everything once, it can dehydrate the local copy — the files appear in the junction but only download on demand. Right-click any file or folder › Free up space. Files at the original D:\ path remain real (not dehydrated).
• Junctions and Files On-Demand can interact oddly. If apps that read the original path see “cloud-only” placeholder behavior they may misbehave. Do not enable Files On-Demand on the junction if applications open the files through the OneDrive path. Use it only when apps go through the original (D:\) path.
• OneDrive size limits still apply. Your tenant has a per-user storage cap (typically 1 TB or 5 TB depending on plan); make sure you have headroom.
• Per-file size limits. Single files larger than 250 GB will not sync. Most clients never hit this; CAD and video shops sometimes do.
• Excluded file types and length limits. OneDrive will not sync filenames longer than 256 characters or paths longer than 400. Older PSTs and Outlook archive files can also be problematic. We can audit a folder before you light up the junction if you have legacy data.
• Removing the junction is safe. If you ever change your mind, delete the junction folder from File Explorer (or run rmdir "C:\...\BackupLink-Customers"). The original files are untouched. OneDrive will mark the cloud copy as deleted — if you want to keep the cloud copy, move it out of the OneDrive recycle bin within 30 days.

What about network drives?

If the data lives on a NAS or file server (UNC path), junctions will not follow it — OneDrive will refuse to sync. For network-share backup we recommend a different approach: a dedicated backup product (Veeam, Datto, Acronis, etc.) that can read the share and back up to cloud storage on its own schedule. OneDrive is designed to back up the user’s own working files; it is not a substitute for proper server backup.

That said, you can use the trick the other direction: if a network folder is mapped to a drive letter, you can copy / mirror its contents into a OneDrive subfolder with robocopy on a schedule. That is a valid “poor-man’s backup” for small departmental shares. Talk to us if you want a worked example.

Doing this for several machines / a whole office

Manually running mklink on every workstation is fine for one or two machines, but for a fleet we package it as a Group Policy or Intune script so the junctions are recreated automatically when a user signs into a new workstation. Same trick, just managed.

If you want us to roll this out across an office — or just check whether your current OneDrive setup is actually backing up the data you think it is — drop us a line or call 970-282-8838.