When a customer pays — online by card or bank, on a tech's phone, or with cash or a check the office records — Run a Call records a payment in QuickBooks Online against the matching invoice, so the invoice shows as paid in both places.
When a payment goes to QuickBooks
- Right away, when the payment is recorded: an online payment clears, a tech collects in the field, or someone in the office records cash or a check.
- The hourly sync catches anything that didn't go through the first time.
The Payments switch under Sync settings & account mapping → Sync Settings must be on.
Order matters
A payment can only be applied once its invoice — and that invoice's customer — are in QuickBooks. If they aren't yet, Run a Call sends them first. If one of them is held back (for example the customer is waiting for a QuickBooks match), the payment waits with "waiting on a related record to sync first" and goes over by itself as soon as the invoice clears. Nothing is lost while it waits.
What carries over
| Run a Call | QuickBooks |
|---|---|
| Amount | Payment amount |
| Date collected | Payment date |
| The invoice it pays | Applied to that invoice |
| Payment method (Cash, Check, Card, a custom method…) | Payment method, using the mapping on the Payment methods card (details). If no matching QuickBooks method is found, the payment is recorded without one. |
| Check or reference number | Reference no. |
| "Paid by" name, when someone other than the customer paid | Memo: Received from … |
Run a Call doesn't choose a deposit account, so QuickBooks puts the money where it normally does for received payments — typically Undeposited Funds / Payments to deposit — until you record the bank deposit in QuickBooks.
One check for several invoices
When you record a single payment across several invoices from the customer's profile (One payment across several invoices), QuickBooks gets one payment per customer applied to each invoice, all sharing the check number — so it still becomes a single line when you make the deposit.
What stays in QuickBooks
- Deposits and processor payouts. Match Stripe deposits in QuickBooks the way your bookkeeper already does.
- Deleted payments. If you remove a payment in Run a Call, delete the matching payment in QuickBooks yourself.
Refunds, credits and card fees
Once you've chosen the accounts under Refunds and card fees, these sync too: refunds post as refund receipts, credits as credit memos, applied credits as zero-dollar payments, and card fees customers pay as a Card processing fee line on their own income account. Until the accounts are chosen, they wait with QuickBooks needs your decision. See Card fees and refunds in QuickBooks Online.
Payments that don't sync on purpose
Payments on invoices that came over from your previous software aren't sent, because QuickBooks already has those invoices. Reconcile them in QuickBooks.
When a payment is held back
It appears on the QuickBooks page under records that need attention with the reason and the fix — most often the invoice ordering above or a deleted QuickBooks account. Fix the cause, then Retry. See Resolving common QuickBooks errors.