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Sync specific payments and refunds to QuickBooks when you need manual control over your accounting records.

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When you need this

Use manual sync when:
  • QuickBooks connection was set up after payments were processed
  • You want to sync only specific transactions
  • Automatic sync failed for individual payments
  • You need to control timing of accounting entries
Manual sync requires an active Pro subscription and QuickBooks Online connection. Set up QuickBooks integration first in Settings → Integrations.

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Sync a payment

  1. Go to an invoice with payment activity
  2. Find the payment in the Payment Activity table
  3. Click Sync Payment next to the payment
  4. Wait for sync to complete (button shows loading spinner)
What happens next: The payment syncs to QuickBooks as an invoice, payment record, and bank deposit. The sync button disappears and shows a QuickBooks icon.

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Sync a refund

  1. Go to an invoice with refund activity
  2. Find the refund in the Payment Activity table
  3. Click Sync Refund next to the refund
  4. Wait for sync to complete
What happens next: The refund syncs to QuickBooks as a refund record. You’ll see a QuickBooks icon showing the sync is complete.

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Prerequisites

Before syncing payments, verify these settings in QuickBooks integration:
  • Deposit bank account: Where payments are deposited
  • Fee expense account: For processing fees
  • Refund bank account: For refund transactions (refunds only)
Missing account mappings will cause sync to fail. Check your QuickBooks integration settings if sync doesn’t work.

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Common issues

  • Sync button not visible: Check you have Pro subscription and QuickBooks connected
  • “Already synced” error: Payment was previously synced to QuickBooks
  • “Invoice already paid” error: QuickBooks invoice has zero balance remaining
  • Account mapping missing: Set up required bank and expense accounts in QuickBooks settings

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What gets created in QuickBooks

For payments:
  • Invoice record (if not already exists)
  • Payment record linked to invoice
  • Bank deposit with fee deductions
For refunds:
  • Refund record
  • Bank account deduction

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Limitations

  • Can only sync payments with valid amounts greater than $0
  • Previously synced payments can’t be synced again
  • Requires customer email to match or create QuickBooks customer
  • Stripe fees and flashquotes fees are automatically calculated and recorded
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