If invoices or payments aren't showing up in QuickBooks, work through these checks in order. Most of the time the answer is on one page, and nothing is lost — Run a Call holds records back safely until the problem is fixed.
Who can do this: the account owner (QuickBooks settings are owner-only).
Open the QuickBooks page
Go to Settings → Integrations and click Manage on the QuickBooks Online card.
Check the connection card
| You see | What to do |
|---|---|
| Token expired with a Reconnect button | QuickBooks signed Run a Call out. Click Reconnect and sign in to QuickBooks. Syncing resumes where it stopped. |
| A banner: Hourly sync is paused — review, then turn it on | Sync was paused after a QuickBooks history import so you could check it first. Click Looks good — turn on hourly sync. |
| Last sync is recent and Auto sync: Every hour | The connection is fine. Go to step 3. |
Sync runs every hour. A record you created a few minutes ago may just be waiting for the next run — its status shows pending.
Look at what's held
Under Your books, reconciled, each record type shows chips: in QuickBooks, on the way, need a decision and we're on it. If anything is held, a list appears below — "N records need your decision" when something is waiting for you, or "N records we're looking into" when nothing is — grouped by cause.
- need a decision (red) — something only you can decide. Follow the What to do line, then click Retry on the record (or Retry all).
- on the way / we're on it — nothing for you to do. On-the-way records go over on their own once a related record syncs; we're-on-it records are being looked at on our side.
Every number on the page comes from the same count — the badge in the settings menu, the Integrations card and the list always agree.
Check your account and tax mapping
Many held invoices come down to setup. Open Sync settings & account mapping and confirm:
- An Income Account is picked, and it still exists and is active in QuickBooks.
- If you charge sales tax, a Tax Code is picked — and, if you use more than one rate, each rate is mapped under Tax codes by jurisdiction.
Click Save Settings. Saving a tax code or class re-queues invoices that were waiting on it.
Common situations
| Situation | Likely cause | Fix |
|---|---|---|
| "Nothing has synced since yesterday" | The QuickBooks connection expired | Reconnect |
| "Only taxed invoices are missing" | No tax code, or a tax rate isn't mapped | Map it under Sync settings & account mapping, then save |
| "A customer never shows up in QuickBooks" | A customer from your old software has no QuickBooks match | Create or rename the customer in QuickBooks to match, then open and save the customer in Run a Call |
| "The Sync Log says Skipped" | Invoices and payments migrated from your old system — QuickBooks already has them | Nothing to do |
| "An old invoice was refused" | Its date is before your QuickBooks closing date | Open Details on the record and check with your accountant |
Disconnecting and reconnecting doesn't "reset" syncing. Reconnecting the same QuickBooks company keeps every link, so nothing is sent twice — but it doesn't fix a record that QuickBooks refused either. Use Reconnect when the token expired; for a stuck record, open Details and fix the cause shown there.
Still stuck?
Click Details on the record, copy the text, and send it to us from Settings → Support. See Getting help from Run a Call support.