QuickBooks Payments groups the payments you process in a single day into one bank deposit, so the clean way to handle a batch is to match that one downloaded deposit to its multiple payment records right in the bank feed, no Merchant Center workaround needed. You don't want to exclude these to clear them, since excluding removes them from your books, while matching is what links everything correctly.
Step 1: Match the batch deposit to its payments
- Go to All apps, then Accounting, then Bank transactions.
- Find the downloaded batch deposit and select it to expand it.
- Choose Match (or Find match / Find other matches).
- Check the box next to each payment or invoice that makes up the batch.
- Confirm the selected total matches the deposit, then select Match.
Full steps: Match your bank and credit card transactions in QuickBooks Online.
If the Match option isn't showing
Two common reasons, with quick fixes:
- It's often a browser hiccup on the bank transactions page. Try an incognito or private window, or switch to another supported browser, and check again.
- If you're on an older banking layout, use Find match (or Find other matches) on the transaction in the review tab instead, then select the multiple records.
About the amounts not matching (processing fees)
QuickBooks Payments usually deposits your money after taking out processing fees, so a batch deposit's amount often won't equal the sum of the invoices. When that happens, account for the fee so the match balances rather than forcing it. The article below walks through comparing your Merchant Service Center deposit list to your bank statement and handling the fee so the deposit ties out: Fix QuickBooks Payments deposits to match your bank statements. For grouping payments and adding a bank/processing fee line to a deposit, see Record and make bank deposits in QuickBooks Online.
A note on Pending, and on Exclude
Deposits still in the Pending state are ones QuickBooks is still processing, so they shouldn't be on your bank statement yet and don't need to be cleared manually. And please don't Exclude a real QuickBooks Payments deposit just to get it out of the list, since excluding keeps it off your books and will throw off your income and reconciliation. If some payments deposits didn't record automatically, this article helps: Fix the alert that some QuickBooks Payments deposits weren't automatically recorded.
If Match still won't appear after trying a clean browser, reply with what you see when you expand the batch deposit and we'll help you sort it out.
