# How to Receive Payments and Apply Them to Invoices in QuickBooks Desktop > Record customer payments against open invoices in QuickBooks Desktop, handle partial payments, and move Undeposited Funds into a bank deposit. - URL: https://logistify.ai/guides/quickbooks-desktop/receive-payments-apply-to-invoices/ - Section: QuickBooks Desktop Guides, Receivables - Applies to: QuickBooks Desktop Enterprise, Premier, Pro, Accountant - Steps checked against: Intuit's QuickBooks Desktop help articles, updated August 2026 - Updated: 2026-10-18 **Short answer:** In QuickBooks Desktop, go to Customers > Receive Payments, choose the customer in Received From, enter the amount, and check the invoices it pays. By default the payment goes to Undeposited Funds. When the money reaches the bank, select Record Deposits / Make Deposits on the Home page to combine those payments into one deposit. This works in Pro, Premier, Enterprise and Accountant. ## Before you start - The invoice has to be in QuickBooks first. Receive Payments applies money to open invoices. - Check your payment preferences at Edit > Preferences > Payments > Company Preferences. - With Automatically apply payments on, QuickBooks applies each payment to the oldest open invoice. Turn it off if you'd rather pick invoices yourself. - Use Undeposited Funds as a default deposit to account is on by default. It holds payments until you record the bank deposit. - If you take payments through QuickBooks Payments, QuickBooks records them and creates the deposits for you. This guide covers checks, ACH and wires you record yourself. ## Step 1: Record the payment 1. Go to Customers > Receive Payments, or select Receive Payments on the Home page. 2. In Received From, choose the customer. 3. Enter the amount received, check the date, and choose the payment method. 4. Enter the check or reference number, so the payment is easy to find later. 5. Check each invoice the payment covers. If the remittance lists invoices, follow it rather than the oldest-first default. 6. Select Save & Close. ## Step 2: Handle a payment that doesn't match the invoice ### The customer paid less than the invoice 1. Enter the amount the customer actually paid and check the invoice. 2. When QuickBooks shows the underpayment, select Leave as Underpayment. 3. Select Save & Close. The invoice stays open for the rest. If you'll never collect a small leftover balance, write it off instead. Select Discounts and Credits, open the Discount tab, enter the amount, and choose the Discount Account. Ask your accountant which account to use. ### The customer paid more than the invoices Enter the full amount and check the invoices it pays. When QuickBooks asks about the extra, select Leave the credit to be used later. The remainder stays as a credit for that customer. Apply it to a later invoice from Discounts and Credits, or refund it, as covered in how to [create and apply credit memos](https://logistify.ai/guides/quickbooks-desktop/create-apply-credit-memos/). ## Step 3: Deposit the payments 1. On the Home page, select Record Deposits / Make Deposits. 2. In Payments to Deposit, select the payments on your deposit slip or bank line, then select OK. 3. In Make Deposits, choose the bank account in the Deposit to dropdown. 4. Enter the date the money reached the bank, and check the total against the slip. 5. Add a memo if you need one, then select Save & Close. Make one deposit for each deposit slip, so QuickBooks matches the bank. Only payments sitting in Undeposited Funds appear in Payments to Deposit. A payment that shows up alone on your bank statement has nothing to combine with. It can go directly to the bank account instead. ## Fix common mistakes - Payment on the wrong invoice: open that invoice, then the Reports tab > Transaction History. Select the payment and Go To, move the checkmark to the right invoice, and save. - Full payment recorded for a partial one: find the payment the same way and change the amount to what you received. - Payment deposited straight to the bank while the invoice stays open: edit the deposit so Received From is the customer and From Account is Accounts Receivable. - Then apply that credit in Receive Payments > Discounts and Credits. Check with your accountant first, especially if the period is closed. - Old payments stuck in Undeposited Funds: go to Lists > Chart of Accounts, right-click Undeposited Funds and choose QuickReport. Set Dates to All, then filter Cleared to No in Customize Report. - A deposit built wrong: find it in the Deposit Detail report (Reports > Report Center > Banking). Fix it, or delete it to send its payments back to Undeposited Funds. ## Where QuickBooks Desktop leaves the work to you - Someone has to match each bank line to a customer and the invoices it pays. The remittance often arrives by email or PDF, apart from the money. - Short payments and overpayments need a decision: chase the balance, write it off, hold a credit or refund it. - Applying to the oldest invoice by default can hide a dispute on one specific invoice. - Undeposited Funds only ties to the bank if deposits are grouped the way the bank grouped them. ## How Logistify helps with cash application The [Accounts Receivable Service](https://logistify.ai/agents/accounts-receivable/) does the matching. It matches customer payments in the bank file to the open invoices they pay and records them in QuickBooks Desktop as Receive Payments. Unclear payments, short payments and overpayments are left for your team. We explain the approach in [AI cash application for QuickBooks Desktop Enterprise](https://logistify.ai/blog/ai-cash-application-quickbooks-desktop-enterprise/). If you're weighing a general AI chatbot instead, read [whether a general AI chatbot can do accounts receivable in QuickBooks Desktop Enterprise](https://logistify.ai/blog/can-chatgpt-or-claude-do-accounts-receivable-quickbooks-desktop-enterprise/). ## Frequently Asked Questions ### Why do customer payments go to Undeposited Funds? So you can combine several payments into one deposit that matches your bank statement. You can turn the default off at Edit > Preferences > Payments > Company Preferences. ### How do I record a partial payment on an invoice? Enter the amount received in Receive Payments and check the invoice. Select Leave as Underpayment, and the rest stays open on the invoice. ### How do I stop QuickBooks applying payments to the oldest invoice? Go to Edit > Preferences > Payments > Company Preferences and clear Automatically apply payments. Then check the invoices yourself on each payment. ### Can one payment pay several invoices? Yes. Check every invoice the payment covers in Receive Payments before you save. ## Sources - [Intuit: Record an invoice payment in QuickBooks Desktop](https://quickbooks.intuit.com/learn-support/en-us/help-article/accounts-receivable/record-invoice-payment/L9bczboPR_US_en_US) - [Intuit: Deposit payments into the Undeposited Funds account in QuickBooks Desktop](https://quickbooks.intuit.com/learn-support/en-us/help-article/bank-deposits/deposit-payments-undeposited-funds-account-desktop/L0MPCun2P_US_en_US) - [Intuit: Record and make bank deposits in QuickBooks Desktop](https://quickbooks.intuit.com/learn-support/en-us/help-article/bank-deposits/record-make-bank-deposits-quickbooks-desktop/L2R3J0uic_US_en_US) - [Intuit: Resolve common issues when applying a payment towards an invoice](https://quickbooks.intuit.com/learn-support/en-us/help-article/accounting-bookkeeping/resolve-common-issues-applying-payment-towards/L2UMXN8tt_US_en_US) - [Intuit: Write off customer and vendor balances](https://quickbooks.intuit.com/learn-support/en-us/help-article/vendor-management/write-customer-vendor-balances/L738xKfuq_US_en_US) - [Intuit: Get started with customer transaction workflows in QuickBooks Desktop](https://quickbooks.intuit.com/learn-support/en-us/help-article/accounts-receivable/get-started-customer-transaction-workflows-desktop/L3pkPaW5h_US_en_US) - [Intuit: Mastering QuickBooks Desktop Level 1 learning manual (PDF)](https://quickbooks.intuit.com/oidam/intuit/sbseg/en_us/priority-circle/content/QBD-Level1-Manual-2021.pdf)