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Home » QuickBooks Merchant Services Not Working: Fix These 5 Issues

QuickBooks Merchant Services Not Working: Fix These 5 Issues

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Is QuickBooks Merchant Services not working, or do you get an error when recording a deposit? Often, QuickBooks users may find themselves unable to record or match Merchant Services activity and receive messages like:

Please wait. We’re matching your deposits to QuickBooks Desktop records.

or

A payment you are trying to download cannot be matched or recorded

or

Unrecoverable error XXXXX XXXX

To address that, we are going to explore different instances when the users find QuickBooks Merchant Services not working. 

Depending on the unique circumstances, we have compiled different sections for:

  • QuickBooks Can’t Record or Match Merchant Service Deposits
  • Error When Recording Merchant Service Activity
  • Unrecoverable Error When Trying to Record Merchant Service Deposits
  • If the Merchant Service Deposit Link is Not Working
  • There was an error communicating with the QuickBooks Payments Service (Mac)
  • Other Issues Related to QuickBooks Payments (Merchant Services)

Therefore, move to the section that best fits your query and follow the instructions given there.

Although this guide will prove very helpful for self-re troubleshooting, for a faster resolution, we recommend that you connect to a QB ProAdvisor. Dial 800-580-5375

Table of Contents

Section 1: QuickBooks Can’t Record or Match Merchant Service Deposits

In this section, we will see how to troubleshoot issues with recording or matching Merchant Service deposits.

If the Merchant Service Deposit does not match and record the deposits, ensure the auto-matching and record settings are enabled.

Turn ON Auto-Matching & Record Settings

Let us turn on auto-matching to get QuickBooks

  • Click on the Banking menu.
  • Select Record Merchant Service Deposits.
  • Choose Change your deposit settings.
  • Now, turn on or enable the Auto match & record settings.
  • Finally, select Save.

If you can’t find the payments to deposit or match them, check the undeposited funds account.

The deposit speeds and status depend on your QuickBooks product. It might take longer for your deposit to show in QuickBooks. You can check the Merchant Service Center to see when a deposit was made.

  • Go to the Activity & Reports tab, followed by All Statements.
  • Locate the transaction you want to check. Choose View.
  • Type in the last 4 digits of the Tax ID number.
  • Go to Activity Summary. See on what date the deposit was made.

You can also view the status of all your processed payment transactions in the Merchant Service Center.

  • Open the Merchant Service Center and sign in.
  • Go to the homepage and choose Activities & Reports.
  • Select Deposits.
  • Go to the Dates field and select the date range.
  • Click on Search.

You can also check your bank’s website for more details on the payment.

Open QB Desktop and run Merchant Services. If you face an issue, try the methods given in the next few sections.

Section 2: Error When Recording Merchant Service Activity

Sometimes, while you attempt to record Merchant Services activity, you see this error below:

Please wait. We’re matching your deposits to QuickBooks Desktop records.

Error: Please wait…We’re matching your deposits to QuickBooks Desktop records

Some users have reported that when they select Merchant Service Deposits, the Record Merchant Service Deposits, followed by a loading sign, and this message:

Please wait…We’re matching your deposits to QuickBooks Desktop records

The process gets stuck, and the users are not able to record Merchant Service deposits.

Let us see how to resolve it.

1.     Update QuickBooks Desktop

We recommend that you first update your QuickBooks Desktop and mark the Reset Update checkbox when you do so.

Once you are done, restart the QB Desktop. If QuickBooks Merchant Services not working still, continue to the next step.

2.     Disconnect and Reconnect Your Merchant Service Account

 Let us try disconnecting the Merchant Service account from QuickBooks Desktop and connecting it again.

Here is how you can disconnect your QuickBooks Payment (Merchant Service) account.

  • Select Edit.
  • Choose Preferences.
  • Tap on the Payments menu.
  • Now, disconnect the Merchant Service account.

Go along with the instructions or prompts to finish the process.

Here is how you can connect the QuickBooks Merchant Services (QuickBooks Payments) account

  • Open QB Desktop and navigate to the Customers menu.
  • Tap on Link Payment Service to Company File. If a message about credit card protection appears, fill in the fields and tap on OK.
  • Provide the ID and password for QuickBooks Payments. Tap on Sign In.
  • Choose Connect. (Alternatively, if you want to transfer your payments account to another company file, tap on Transfer. Select Yes, transfer.)

Once you connect the Merchant Service account, an icon will appear on the homepage, indicating that you have signed in and are connected to QB Payments.

3.     Turn Off Auto-Matching & Record Settings

Let us turn off auto-matching to get QuickBooks

  • Click on the Banking menu.
  • Select Record Merchant Service Deposits.
  • Choose Change your deposit settings.
  • Now, turn off or disable the Auto match & record settings.
  • Finally, select Save.

Once done, restart QuickBooks Merchant Services and see if everything works fine.

However, if the issue persists, repair your QuickBooks program. For that, first download and install QuickBooks Tool Hub and then follow the steps given below.

  • Open QB Tool Hub.
  • Go to the Program Problems tab.
  • Choose Quick Fix my Program.
  • Go back to QB Tool Hub.
  • Navigate to the Program Problems tab.
  • Choose QuickBooks Program Diagnostic Tool.

Now, restart QB Desktop and see if the QuickBooks Merchant Services not working issue is resolved. If the problem persists, follow the methods given in section 3.

Error: A payment you are trying to download can not be matched or recorded

Other times, the users see this error message on the screen:

A payment you are trying to download can not be matched or recorded

Here are some reasons why you can’t match or record payments in Merchant Service

  • The invoice might be already partially or fully paid
  • The invoice you want to modify might have yet to reach the closing date
  • There might be damage in the payment method or “Check” payment method in QB
  • There might be issues with the Accounts Receivable

1.     Check if the Invoice is Already Paid

It might so happen that the invoice might be already paid, partially or fully, and that is why you can’t record or match payment.

If that is the case, here is what you need to do:

  • Locate the invoice that gives way to the error.
  • Unapply or void all the payments to the invoice, if any. This will make the full payments to the invoice due.
  • Now, close Merchant Service Deposits and relaunch it.

Now, attempt to record the payments in QuickBooks Merchant Services

2.     Check if the Invoice is Before the Closing Date

Let us check if the invoice is still before or on the closing date.

  • Close Merchant Service Deposits.
  • Sign in to the QuickBooks company data file as admin.
  • Tap on Edit, and choose Preferences.
  • Select Accounting.
  • Go to the Company Preferences tab.
  • Choose Set Data/Password. Now, change the closing date as required.
  • Click on OK twice and save the changes in the closing date and the preferences.

Now, go back to Merchant Service Deposits and try recording the payment again.

3.     Check for Damaged Payment Methods

Let us check if the reason QuickBooks can’t record or match payments is because of a damaged payment method.

  • Tap on Lists. Choose Customer & Vendor Profile Lists.
  • Click on Payment Method List.
  • Ensure that all the details for Payment Methods and Payment Types are correct.
Payment MethodType
American ExpressAmerican Express
CashCash
CheckCheck
DiscoverDiscover
E-CheckE-Check
MasterCardMasterCard
Debit CardDebit Card
VisaVisa
Gift CardGift Card
  • If required, make changes to any incorrect Payment Methods or Types.

Now, go back to QuickBooks Merchant Services and record payments again.

1.     Check for a Damaged Check Payment Method

If you can record credit card payments normally, but Check payments don’t, there might be damages in the Check payment methods.

 You can change the payment method to a credit card.

  • Tap on Lists. Choose Customer & Vendor Profile Lists.
  • Click on Payment Method List.
  • Double-tap on Check.
  • Change the Payment Type to any credit card type, such as Visa.
  • Choose OK.

Now, the QuickBooks Merchant Services should work fine and allow payments to be recorded.

2.     Troubleshoot Accounts Receivable Issues

If you find QuickBooks Merchant Services not working, let us check if it is because of issues with accounts receivable, such as:

  • There is a damaged receivable account in the QB file
  • There are multiple Accounts Receivables in the chart of accounts
  • Invoices might be saved against Accounts Receivable sub-accounts.

Let us explore these aspects one by one.

a.     There is a damaged receivable account in the QB file

To fix this, you can merge your existing Accounts Receivable account into a new one.

  • Tap on Lists and choose Chart of Accounts.
  • Go to the Account menu at the bottom and choose New.
  • Tap on Other Account Types and select Accounts Receivable.
  • Click on Continue.
  • Provide the Account Name as “Accounts Receivable 2“. Choose Save & Close.
  • Now, right-click on the older Account Receivable account. Choose Edit Account.
  • Rename it to “Accounts Receivable 2” and click on Save & Close.
  • When asked, choose Yes to merge the accounts.
  • Once the merge is completed, you can rename the “Accounts Receivable 2” back to any name you like or the original name.

Now, load the Merchant Services Deposits window and attempt to record the payments again.

b.     There are multiple Accounts Receivables in the chart of accounts

If there are multiple accounts receivables in your chart of accounts, merge the accounts. For this, follow the instructions in the previous step (a) and rename the accounts receivables to the same name.

c.     Invoices might be saved against Accounts Receivable sub-accounts

Let us check if the accounts selected in the invoices are accounts receivables or their subaccounts.

  • Tap on Lists and choose Chart of Accounts.
  • Find the Accounts Receivable account.
  • Select the invoice you faced an issue with when applying for the payment and open it.
  • View which Accounts Receivable account is chosen.
  • If a sub-account is selected, change it to a suitable parent Accounts Receivable account
  • Tap on Save & Close.

Moreover, there has been a Payments Server update, which has fixed various issues with QuickBooks Merchant Services. You can also dismiss transactions.

Section 3: Unrecoverable Error When Trying to Record Merchant Service Deposits

Sometimes, users see an unrecoverable error when they try to record Merchant Service deposits in QB Desktop.

There are several reasons why this happens, such as:

  • The user is trying to make the deposit with a merchant account that lacks full admin rights
  • The merchant account used to make the deposit is signed into multiple workstations
  • QuickBooks program is damaged
  • The company file is corrupt, or has data damage

Let us see how to resolve unrecoverable errors when recording QuickBooks Merchant Services activity.

1.    Assign Full Admin Rights to Merchant Account User

Here is how you can assign full admin rights to the Merchant Account you are using.

  • Open merchantcenter.intuit.com and login to it.
  • Choose Accounts, and tap on Users.
  • Give full admin rights to the user in question.
  • Now attempt to record the Merchant Service Deposits once again.

However, if you still find the QuickBooks Merchant Services not working, continue to the next solution.

2.    Ensure the Merchant Account Isn’t Signed on Multiple Workstations

QuickBooks Merchant Services Deposit won’t work if the merchant account you are using is signed on multiple workstations.

Ensure the merchant account is only logged in one workstation. However, if the QuickBooks Merchant Services not working issue persists, proceed to the next step.

3.    Resolve Data Damage

Let us check for the data damage in the company file and fix it. For that, run verify and rebuild utility on the company file.

However, if the Merchant Services still fails to work, let us repair the QuickBooks Desktop.

4.    Repair QuickBooks Desktop

There are two ways to repair QuickBooks Desktop using QuickBooks Tool Hub. One is through Quick Fix my Program and QuickBooks Program Diagnostic Tool which fixes the program problems. Then there is the QuickBooks Install Diagnostic Tool, which resolves the installation issues.

Repair QuickBooks Desktop, first using Quick Fix my Program and QuickBooks Program Diagnostic Tool, and after that using QuickBooks Install Diagnostic Tool.

Restart your computer and reopen QB Desktop. Check if the QuickBooks Merchant Services not working issue is resolved.

5.    Clean Install QuickBooks Desktop

If the above troubleshooting methods don’t address the problem, the only resort left is to clean install QuickBooks.

Clean install QB Desktop and see if you can use Merchant Services now.

Check how to resolve other instances of the unrecoverable error in QuickBooks Desktop.

Section 4: If the Merchant Service Deposit Link is Not Working

Is the deposit link in QuickBooks Merchant Services not working, and are you unable to record payments?

You can match payments manually. However, first, you need to turn off automatic matching.

a.    Turn Off Automatic Matching

Here is how you can turn off auto matching to get QuickBooks

  • Click on the Banking menu.
  • Select Record Merchant Service Deposits.
  • Choose Change your deposit settings.
  • Now, turn off or disable the Auto match & record settings.
  • Finally, select Save.

b.    Manually Match and Record Payments

Here is how you can manually match and record the payments.

  • Click on the Banking menu.
  • Select Record Merchant Service Deposits.
  • Choose Add Payments to record tab.
  • Tap on the small arrow icon beside the first deposit on the list.
  • Verify the payments in QuickBooks.
  • Choose Add Payments in the Action column to add payments to the bank deposit.
  • Compare the deposit total in QuickBooks with the deposit for that day on your bank statement.
  • After everything matches, choose Save and Close.
  • Verify each bank deposit on the list.
  • After adding all the payments to a bank deposit, select Record Deposit.

Section 5: Error Communicating with the QuickBooks Payments Service (Mac Issue)

QuickBooks Desktop for Mac users might get an error message like the one given below when enabling the ACH e-invoice option.

There was an error communicating with the QuickBooks Payments Service.  Please try again later.

To begin with, update your QuickBooks Desktop for Mac to the latest release. This is because the issue might be caused by a bug or technical glitch, for which the developers would have released fixes by the time you read the blog.

Once you are done, check if you can carry out the operations in Merchant Services without an error.

You can consider processing credit card payments within the company file for your QB Desktop (Mac).

  • Tap on the Customers menu.
  • Select Receive Payment. This will apply the payments to an invoice.
  • Provide the customer and transaction information.
  •  Go to the credit card Payment Method (Pmt. Method).
  • Tap on OK, Charge, or Save, whichever is required to process the transaction.
  • In case you are choosing Visa, MC, AMEX, or Discover, enter the credit card info required in the window you see. Finally, click on the Process option

Other Issues Related to QuickBooks Payments (Merchant Services)

Let us take a look at the major problems users face when using QuickBooks Merchant Services.

1.    The Payment Link is Not Working for the Customers

Sometimes, QuickBooks payment links don’t work, and thus the customers are not able to make payments to the invoices.

Learn how to fix it if the QuickBooks payment link stops working with the help of our subject-specific guide.

2.    QuickBooks Payments are Not Deposited

Often, QuickBooks payments show as paid but are not deposited. To fix this, check the status of your payments and the Undeposited Funds account. For detailed troubleshooting steps, consult our guide on the QB payments not deposited subject.

Wrapping It Up

This was all on how to resolve issues that come up when using Merchant Services. We explored different instances when is QuickBooks Merchant Services not working and how to troubleshoot that.

However, even after carrying out the solutions given, if the problem persists or you have a query, speak to a QB ProAdvisor. They will help you resolve all QuickBooks issues quickly. Dial 800-580-5375!

Top Queries from QuickBooks Users

How do I activate Merchant Services in QuickBooks?

To activate Merchant Services, log into QBO as an admin and choose Account and Settings. Now, click on Payments and go to the Existing Account section. Tap on Connect or Link Merchant Service.

How do I access the Merchant Service Center on QuickBooks desktop?

Let us show how you can open the Merchant Service Center in QuickBooks Desktop. Go to the Customers menu and choose Credit Card Processing. Now, choose Merchant Service Center.

Why is my Intuit QuickBooks not working?

QuickBooks Desktop might not work properly if there is an issue with the program or the company file. To fix that, use QuickBooks Tool Hub to repair your QuickBooks program and search your company file for data damage.

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