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Level 1

Credit card payments not reconciling QB Desktop

A few months ago, we changed the company name. Same EIN, address, phone, bank accounts (names were changed but account #s are the same). The primary email address changed. After multiple QB calls, support and changes (changed the company file named, transferred the merchant account), it seemed OK.

However, now we see credit card payments but cannot "add payment" (get an error with no details) and after a while, they seem to be applied to the invoice. But then they show up in the "record deposit" window, which they never did before. They were always transparently deposited. When I tried to deposit one in the "record deposit" window, all of a sudden, I had a duplicate deposit. Apparently, it deposited itself somehow.

Something isn't right between the merchant account and QB Desktop 2020. The merchant account doesn't auto-apply the payment and won't let me apply it. Then later, things look applied but there are deposits to make. Then later, sometimes, deposits are done. 

Does anyone know how to fix issues like this?

4 Comments 4
QuickBooks Team

Credit card payments not reconciling QB Desktop

Hi there, @SLPOnline. I'm here to help you get this sorted out.


Is your deposit account connected to online banking? QuickBooks deposits and records customer payments for you if auto-matching is turned on from your deposit settings. Follow these instructions to review this setting:

  1. Go to the Banking menu and select Record Merchant Service Deposits.
  2. Select Change your deposit settings.
  3. Check if the Auto match & record setting is on.
  4. Select Save.


If your deposit account is linked to banking feeds, make sure to match them with the deposits.


Be sure to come back if you need more assistance with your customers deposits. I'm here to ensure your success.

QuickBooks Team

Credit card payments not reconciling QB Desktop

Hi @SLPOnline,

Hope you’re doing great. I wanted to see how everything is going about your customer payments. Was it resolved? Do you need any additional help or clarification? If you do, just let me know. I’d be happy to help you at anytime.

Looking forward to your reply. Have a pleasant day ahead!

Level 2

Credit card payments not reconciling QB Desktop

Things are different and I'm not sure if it's a feature or a problem. Once we download online payments, even when they show an error, several hours later they do get applied to invoices and are deposited. Even though they were paid several days ago and even though they're already in our bank account, we still get the error when we try to apply a payment to an invoice. Yet, a day later, they're applied and deposited. Prior to the company name change and transferring the merchant account to the new company, we never had this issue. Like I said, weird. It feels like there's a temporary disconnect between the old company name and the new one.

QuickBooks Team

Credit card payments not reconciling QB Desktop

Welcome back to the QuickBooks Community, SuePolinsky. I'll be providing details on how customers' payment or deposit from QuickBooks payments works in QuickBooks. Then, ensure you'll be routed to the right support team to assist you further on this matter. Beforehand, may I ask the exact error message you're referring? I appreciate any further details so I can share an accurate solution.


When you have QuickBooks Payments, QuickBooks Desktop groups the customer payments you process each day. Then, it deposits this grouped set of payments as a single bank deposit into your bank account. QuickBooks handles the accounting for you and records everything on your chart of accounts. Please know that QuickBooks separates payments and fees so you get all the details. They appear as separate transactions on your bank statements.


Then, the customer payment usually reaches your deposit bank account within 2-3 business days of the transaction. It varies on the time you enter transactions, the bank you choose for payments to be deposited. It can also vary on how long it takes the bank to verify and process electronic deposits.


When clients pay online via credit card, the estimated time for payments to deposit is 5-7 banking days. While ACH payments will take a bit longer during your first month. You'll get your payments within 5 days for the first 1 to 4 weeks. For additional information, you may click this article: Find out when QuickBooks Payments deposits customer payments.


If the issue continues to occur, I recommend contacting our Merchants Services Support Team. This team is the best resource for such inquiries, as they're able to request account information. They can also verify the status of the payment and why you're getting an error when we try to apply a payment to an invoice.


Please also refer to this article to see how QuickBooks Payments deposits work in QuickBooks Online: Common questions about payments deposits in QuickBooks Online.


Don't hesitate to post again here in QuickBooks Community if you have additional questions. I'll be right here to help. Have a great day!

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