Reconciling Payments (Check, Card, Stripe)

Reframed from Cathy and Rachelle's April 2026 "Accounting Sequence." Their document itself flags a couple of things as open questions rather than settled fact — this course keeps those flagged as open here too, rather than quietly resolving them one way or the other.

What you did before (MOM + Authorize.net)

• A payment (check, Purchase Order, or credit card via Authorize.net) got tagged to its MOM order using the Authorize.net invoice number as a synthetic check number (e.g. CC23401) — the credit card payment was recorded in MOM as if it were a check payment.
• Daily credit card totals appeared in Authorize.net, with funds deposited to the Checking Account and posted to GL account 41000.
• At month-end, MOM totaled every check and credit card payment entered that month into a GL Posting Report against 41000. If that total didn't match QuickBooks Desktop's 41000, it had to be reconciled by hand — usually caused by an Authorize.net refund that was never recorded back in MOM, or a MOM payment that didn't match what QuickBooks showed.
• For check payments specifically, accounting deposited the check in QuickBooks under 41000 at the point of the actual bank deposit, and the payment then had to be posted to the specific order it paid.
• Website payments via Stripe were entered daily; Sales was notified immediately, and Joan or Micole would then mark the corresponding invoice paid in MOM by hand.

What you do now (APSync)

• The invoice itself starts in HubSpot and syncs to QuickBooks — see How does sync work — so the "does the order total agree with the payment" check now starts from the QuickBooks invoice, not a MOM order.
• Reconciliation is still your job, not something APSync does for you: confirm the invoice exists in QuickBooks and that the total, customer, tax, shipping, and line items look correct; confirm payment status against the actual payment source; reconcile deposits and clearing accounts the way you always have; make manual QuickBooks adjustments when something doesn't match. Full checklist: Start Here for Accounting.
• The Stripe Clearing Account approach Rachelle described is still the right target design — a dedicated bank-type "Stripe Clearing" account in the Chart of Accounts, Stripe sales and fees synced or entered into it daily, bank-feed payouts matched against the clearing account transfer rather than booked as direct sales income, and the clearing account reconciled monthly against the Stripe Payout report's Net Amount.
• Open question, not yet confirmed either way: whether a payment Sales records in Stripe automatically shows as paid on the matching invoice in QuickBooks via the HubSpot integration, or whether that still needs a manual "mark paid" step the way it did in MOM. Rachelle's own notes flagged this as uncertain — treat it as still open rather than assuming it's automatic.
• Authorize.net still needs to be kept running for as long as any part of this flow still depends on it — that hasn't been confirmed as fully retired.

Watch for

• Stripe payouts and clearing account balances
• check deposits
• refunds that exist in the payment processor but not on the invoice
• invoices that have not synced from HubSpot
• customer or product matching errors

If something does not match

Use Submit an Issue and include the invoice number, payment source, amount, and what you expected to see.