QuickBooks Automatically Record Bank Deposits | Stepwise Guide 

Managing your business finances becomes easier when your accounting software works efficiently behind the scenes. One common question many users have is how QuickBooks automatically records bank deposits and whether the process ensures accurate financial tracking. When set up correctly, QuickBooks automatically records bank deposits, reduces manual data entry, and helps prevent duplicate transactions. 

This automation not only saves time but also improves reconciliation accuracy and cash flow visibility. However, understanding how the feature works—and how to fix issues if deposits don’t match—is essential for maintaining clean and reliable financial records in your QuickBooks account.

Why Recording Bank Deposits Accurately Matters?

Recording bank deposits accurately matters because it ensures your financial records truly reflect the money your business has received, which is essential for making informed decisions and maintaining trust. When deposits are recorded correctly, you can reconcile your books with your bank statements, detect errors or fraud quickly, and avoid overstating or understating your income. Accurate deposit records also support reliable financial statements, simplify tax reporting, and help maintain compliance with accounting standards and regulatory requirements. Ultimately, careful recording of bank deposits protects cash flow visibility and strengthens overall financial control.

Learn How QuickBooks Automatically Record Bank Deposits

In this section, you will learn how to enable the feature to automatically record bank deposits in QuickBooks Desktop: 

Step 1: Let QuickBooks automatically record bank deposits

Enable the automatic record matching to make sure QuickBooks deposits and records customer payments automatically for you.

• Go to Banking in the top menu bar.
• Choose Record Merchant Service Deposits.
• Click on Change your deposit settings.
• Now, enable Auto match & record setting.
• Finally, select Save.

QuickBooks now automatically combines customer payments daily and posts them to your chart of accounts for you.

Note: If you prefer to enter everything on your own, leave the Auto match & record feature turned off. We suggest enabling it and letting QuickBooks handle the heavy lifting. However, if you prefer managing it yourself, we’ll explain how to manually match payments at the end.

Step 2: Review automatic bank deposits

If you receive your monthly bank statement automatically, make sure to review the payments in QuickBooks Desktop.

Compare what’s on the bank statement you received and how QuickBooks recorded your bank deposits. Get started with the bank deposits that QuickBooks already matched and recorded. 

• Go to Banking in the menu bar. 
• Choose Record Merchant Service Deposits.
• Move to the Recorded tab.
• Review your first bank deposit on the list. For further details, click on the small arrow icon ▼next to the deposit. This will show you each customer payment that is grouped in the deposit.
• In your bank statement, find the matching bank deposit.
• If the date and total are the same, mark it as cleared on your bank statement. This means QuickBooks has recorded it accurately.
• Review every deposit listed. If you find any deposits in QuickBooks that don’t align with your bank statement, be sure to note the differences.

Tip: Each day, QuickBooks combines all the customer payments you’ve received into a single bank deposit, so only one deposit is recorded per day. When reviewing your bank statement, you’ll just need to match that one daily QuickBooks deposit. Note that QuickBooks lists payments and processing fees separately, so you’ll still see the full breakdown. These will show up as individual transactions on your bank statement.

What to Do If Payments in QuickBooks Don’t Match Your Bank Statement?

In case your QuickBooks transactions don’t match the bank statement, review the specific bank deposits that aren’t matching.

Tip: QuickBooks should align with your bank statement — not the other way around. Most electronic invoice payments are typically accurate. However, payments that remain in accounts receivable or those processed through GoPayments may require additional review.

• Select the Add payments to record tab in the open Record Merchant Service Deposits window.
• Click on the small arrow icon next to a deposit to expand the section. 
• Now, review the payments that are already matching with QuickBooks. This will be named as “Payment added” in the Actions column.
• Check the deposit amount displayed against the amount recorded on your bank statement.
• If the figures are the same, click Add payment in the Action column for any transactions QuickBooks hasn’t included yet to attach them to the deposit. If the amounts differ, do not add any payments.
• Verify the payment information, then click Save and close.
• Go through each deposit listed and include any missing payments that should be part of them.

Next steps: Change how QuickBooks records payments on your chart of accounts

If you want to update how QuickBooks posts bank deposits in your chart of accounts:

• Open the Banking menu and choose Record Merchant Service Deposits.
• Click Change your deposit settings.
• From the Bank for deposits dropdown, pick the account where your payments are deposited. From the Fees account dropdown, choose the account used to track processing fees. Then, select the bank account from which those fees are withdrawn in the Fees Bank for fees withdrawal dropdown.
• Once everything is set up, click Save Settings.

If you’re not sure which accounts to use, reach out to your bookkeeper or accountant for guidance.

Manually Record Bank Deposits for QuickBooks Payments

We suggest allowing QuickBooks to automatically match and record your bank deposits. However, if you prefer to handle it on your own, you can follow the manual process instead.

Important: Choose only one method—either let QuickBooks manage the matching and recording for you, or complete the process manually. Avoid using both approaches at the same time.

Step 1: Turn off automatic matching

If you haven’t already, turn off the automatic matching setting:

• Go to the Banking menu and select Record Merchant Service Deposits.
• Select Change your deposit settings.
• Turn off Auto match & record setting.
• Select Save.

Step 2: Manually match and record payments

When your monthly bank statement arrives, go through the payments in QuickBooks Desktop and compare them to the deposits shown on the statement. Make sure each deposit recorded in QuickBooks matches the deposit listed by your bank for the same date.

• Open the Banking menu and click Record Merchant Service Deposits.
• Go to the Add payments to record tab.
• Click the small ▼ arrow beside the first deposit listed.
• Examine the related payments in QuickBooks.
• In the Action column, choose Add payments to include them in the bank deposit.
• Check that the total deposit amount in QuickBooks matches the amount shown on your bank statement for that date.
• If the amounts agree, click Save and Close to combine the payments into one deposit and post it to your chart of accounts.
• Continue reviewing each deposit displayed in the list.
• After all payments have been added to their deposits, select Record Deposit.

Deposits you’ve already entered will appear in the Recorded tab. Verify that every one of these aligns with what the bank reports.

Note: There’s no need to check deposits in the Pending tab. These transactions are still being processed by QuickBooks and will not yet appear on your bank statement.

Record missing deposits or fees

If you notice deposits on your bank statement that don’t appear in QuickBooks, there’s no need to be concerned. 

When a full day’s deposit is missing from QuickBooks, you can enter it manually. Use your bank statement to ensure the details you enter are accurate.

• Open the Banking menu and choose Make Deposits.
• Click Payments.
• Select the payments that belong to that specific day, then click OK.
• Choose Save & Close to complete the entry.

Conclusion

For accurate bookkeeping and streamlined financial management, QuickBooks automatically record bank deposits when transactions are properly linked and matched within the system. By ensuring your bank feeds are connected and categorized correctly, you can avoid duplicate entries, maintain clean records, and simplify reconciliation.

If the detailed steps do not work for you or you require professional assistance, we recommend consulting a QuickBooks ProAdvisor at QuickBooksSupportNet. Dial +1 (866) 500-0076 and talk to a certified expert now!

Frequently Asked Questions 

How do I record a deposit in QuickBooks Online?

To record a deposit in QuickBooks Online, click the + New button, select Bank Deposit, choose the account, and select the received payments from the list. Ensure the total matches your bank statement to move funds from “Undeposited Funds” to the actual bank account. 

What is record deposit in QuickBooks Desktop?

The Record Deposit feature in QuickBooks Desktop is a function used to combine multiple customer payments (initially held in “Undeposited Funds”) into a single transaction that matches the total deposit shown on your bank statement.

What happens if I deposit multiple customer payments in QuickBooks Online?

Depositing multiple customer payments in QuickBooks Online (QBO) requires grouping them into a single deposit transaction to match your bank statement, usually via the “Undeposited Funds” (or “Payments to Deposit“) account.

Can a bank deposit match a payment in QuickBooks Online?

Yes, bank deposits can and should be matched to customer payments in QuickBooks Online (QBO) to ensure accurate records and avoid duplicate income.

Does QuickBooks automatically deposit into a bank account?

Yes, QuickBooks can automatically deposit funds into your bank account, but this feature requires you to use QuickBooks Payments and for the system to be properly configured. 

Does QuickBooks automatically record transactions?

Yes, QuickBooks can automatically record, match, and categorize bank and credit card transactions once you connect your accounts, reducing manual data entry. It also supports automatic recording of recurring transactions, such as rent, and handles bank deposits/fees automatically if you use QuickBooks Payments.