How do you reconcile payments with QuickBooks?
Match your deposits to unpaid invoices in QuickBooks by using the deposit detail report and comparing it against your invoice list. Most contractors skip this step or do it manually once a month. It takes 15 minutes and keeps your books clean for tax time.
Pull your deposit report first
Go to Reports > Banking > Deposits. Select your date range—most contractors do this monthly. The report shows every deposit that hit your bank account, listed by date with amounts. Write down the deposit dates and totals. If you use digital payment methods like ACH or credit card processing, QuickBooks might show these as separate line items instead of one lump deposit. A 3,500 dollar job paid via ACH appears differently than one paid by check. That's normal. The key is matching the total dollars received to the invoices you issued. Most contractors process deposits twice a week, so your report will have 8-10 entries per month.
Match deposits against your invoice list
Go to Reports > Sales > A/R Aging Summary. This shows which invoices customers actually paid. Cross-reference the deposit report against this aging report. Example: You deposited 2,840 dollars on March 15th. Your A/R aging shows invoice 2301 for 1,200 dollars and invoice 2305 for 1,640 dollars marked as paid that same day. Those two invoices equal your deposit. Record this match somewhere—a spreadsheet, a note in the invoice memo, wherever your system lives. When a single deposit covers multiple invoices, note all the invoice numbers. When one invoice gets paid in chunks (deposit 1,500 dollars this week, 800 dollars next week), track both deposits against that one invoice number.
Record the deposits in QuickBooks
In QuickBooks, go to Banking > Make Deposits. Select the payment method (ACH, credit card, check). Match it to the customer invoice. QuickBooks will auto-mark the invoice as paid once you complete the deposit entry. If you're using digital payments like Square, Stripe, or your bank's ACH system, these often feed directly into QuickBooks as automatic deposits. That cuts your work in half. Check your bank feed in QuickBooks (Banking > Banking tab) to see if payments are already imported. Many contractors miss this because they assume manual entry is required. It's not.
Catch discrepancies before they compound
If a deposit doesn't match your invoices, stop and investigate before moving on. Example: You show a 2,500 dollar deposit but only 2,200 dollars in matching invoices. The 300 dollar difference might be a customer discount, a returned check that re-deposited, or a payment you forgot to invoice. Find it now. Running this reconciliation monthly saves you hours of detective work at year-end when your accountant asks why your revenue report doesn't match your bank statement. If you're handling multiple jobs per deposit, this monthly check is essential. Most contractors who skip reconciliation lose 1-2 days in April doing back-dated work.
Bottom line
Pull your deposit report monthly, match it against your invoice list, then record deposits in QuickBooks. This 15-minute habit keeps your cash flow visible and makes tax season fast.