Disconnecting QuickBooks stops Run a Call from sending anything else to your books. Nothing already in QuickBooks is deleted or changed, and nothing in Run a Call is lost. Run a Call also remembers which QuickBooks record each customer, invoice and payment was sent to, so reconnecting the same company later picks up where it left off.
Only the account owner can disconnect QuickBooks.
Before you disconnect
Ask yourself whether you really need to. Two common situations don't call for it:
- The connection expired. If the QuickBooks page shows Token expired, click Reconnect instead. Your links and settings stay in place and syncing resumes where it stopped.
- You want to pause while your bookkeeper cleans up. Turn off the record types you want to hold under Sync settings & account mapping → Sync Settings instead, then turn them back on later.
Open the QuickBooks page
Go to Settings → Integrations and click Manage on the QuickBooks Online card.
Click Disconnect
In the connection card at the top, click Disconnect.
Confirm
The dialog reads "Disconnect QuickBooks? This will stop all syncing. Data already in QuickBooks will remain. You can reconnect later — reconnecting the same QuickBooks company picks up where it left off, without sending anything twice." Confirm to finish. You'll see "QuickBooks disconnected".
What happens
| After disconnecting | |
|---|---|
| New customers, invoices, payments, items, POs, expenses | Stay in Run a Call only. Nothing is sent to QuickBooks. |
| Everything already in QuickBooks | Untouched — invoices, payments, customers and bills stay exactly as they are. |
| Your QuickBooks access | Run a Call's access to your QuickBooks company is revoked. |
| Links between records | Kept. Run a Call still knows which QuickBooks record each customer, invoice and payment was sent to. Records that were stuck with a sync error are released, so they get a clean retry if you reconnect. |
| Your settings (income account, tax codes, classes, what syncs) | Kept. |
Reconnecting later
Click Connect QuickBooks on the same page and approve the connection again. Because your settings were kept, you go straight back to the health screen and hourly syncing resumes.
What happens next depends on which QuickBooks company you approve:
| You reconnect to | What Run a Call does |
|---|---|
| The same QuickBooks company | Keeps every link. Nothing that is already in your books is sent again. Anything created or edited while you were disconnected syncs on the next run — edits update the existing QuickBooks copy. |
| A different QuickBooks company | Starts from zero for the new books. The old links are retired and your sent invoices, recorded payments, customers and items are sent to the new company. |
Run a Call tells the two apart by the company you pick on the Intuit approval screen. If you keep more than one QuickBooks company, check the name there before you approve.
If QuickBooks stops syncing on its own
Sometimes the connection lapses without anyone clicking Disconnect — for example after a password change on the Intuit side, or when access is removed from inside QuickBooks. When that happens:
- The owner and admins get a "QuickBooks stopped syncing" notification, and the owner gets an email.
- The QuickBooks page shows Token expired and a Reconnect button.
This is not a disconnect: links and settings are kept. Click Reconnect, sign in to Intuit, and everything that queued up in the meantime syncs.
Using QuickBooks Desktop?
On a QuickBooks Desktop connection, Disconnect is on the QuickBooks Desktop card. The confirmation reads "Run a Call stops sending invoices and payments to QuickBooks. Nothing already in QuickBooks is changed." Anything still waiting for the next check-in is dropped; the record links are kept. When you set Desktop up again and your QuickBooks computer checks in with the same company file, nothing already in QuickBooks is sent again. If the company file's location or name changed — a new computer, a renamed file — the QuickBooks Desktop card asks "Is this the same company as before?" Choose Same company, keep links if the file was only moved or renamed, or Different company, start fresh to send everything to the new file. Setup waits for your answer. See Connecting QuickBooks Desktop.