How to Troubleshoot QuickBooks Payments (Merchant Services) Issues

QuickBooks Merchant Services enables businesses to process customer payments efficiently. If it is not functioning, businesses encounter specific issues. These issues include not managing or receiving payments including e-checks, credit cards, etc. The issue occurs when the Merchant Service account links incorrectly or the payment method gets corrupted.

Here is the list of the common QuickBooks Merchant Services error messages:

• “Please wait. We’re matching your deposits to QuickBooks Desktop records.”
• “We’re sorry, but your session ended due to inactivity. Click here to log back in.”

This guide includes the common QuickBooks Merchant Service issues and their troubleshooting steps. Implement the solutions to resolve the issues quickly and restore smooth payment processing.

Identify the Cause Behind the QuickBooks Payments Link Failure.

The QuickBooks Payment link often stops working due to multiple reasons. This impacts both the QuickBooks Online and Desktop versions. Comprehending the reason is vital to avoid future problems.

Here are some of the reasons behind the QuickBooks Payment link failure:

• Excess browser cache and cookies can trigger problems with QuickBooks Online payment links.
• Corrupted or damaged company file.
• Defects in payment links often arise due to an old QuickBooks version.
• The invoice template is old or outdated.
• On the customer invoice, the payment link fails to work.
• In the QuickBooks Desktop or Self-Employed edition, QuickBooks Online payments are deactivated.
• The browser failed to address the system requirements for QuickBooks Online.
• In the Online Delivery option, the invoice link has been changed.
• L3 data processing errors can trigger payment link failures.
• Problems with the payment gateway or internet network can interrupt the payment system.
• Verification issues often stop QuickBooks invoices from accessing the payment gateway.
• Often, the link between Intuit Server and QuickBooks is disrupted by the antivirus or firewall.
• Third-party background applications often trigger disruptions.
• The payment link often malfunctions since QuickBooks Online or Desktop is under maintenance.

QuickBooks Payments issues and How to fix them: An overview

Prior to entering the merchant service deposit, connect the QuickBooks Payments account to the company file. This move guarantees precise organization between company records and payment data. In the absence of this connection, QuickBooks fails to process or record merchant entries.

Here are the steps to link the accounts:

1. In QuickBooks, open the “Customers” menu.
2. Choose the “Link Payment Service to Company File” option.
3. Add the credit card protection details when the prompt appears. Then click the “OK” button.
4. Add the QuickBooks Payments user ID and password.
5. Now, click the “Sign In” option.
6. To create the link, click the “Connect” option.

Once the accounts are linked, review the following issues and steps to resolve them. Every solution aims to resolve a specific issue to return QuickBooks Payments to working order.

1. QuickBooks Desktop Payment Link is Not Working

QuickBooks Desktop often displays errors with the payment link. The link often fails to clear payments or open, and prevents customers from processing invoices online.

Here are the methods to fix the QuickBooks Pay Now link error in the Desktop edition:

Update QuickBooks Desktop

Old QuickBooks versions can lead to payment link errors. Hence, updating the Desktop version to its latest release is the recommended approach:

• Go to the Intuit website.
• Now, choose the “Download and Updates” option.
• From the drop-down menu, select the “QuickBooks Product“.
• Mention the year and version.
• Click the option “Get the latest updates” and then choose the “Save/Save File” option.
• Once the download is over, install the update.
• Reboot the system.

Note: After the update is complete, the payment link must operate properly.

Send the Invoice Email Again

Often, the payment link fails to work for customers, but loads on the device. Once the link is repaired, resend the invoice.

Here are the steps to send the invoice email again:

• Open the QuickBooks Desktop.
• Now, Go to the “Customers” option.
• Check the “Online Payment Options“.
• Select “Change” and choose the payment option preferred.
• Now, click the “Save” option.
• Complete all the invoice details.
• Head to the “Main” tab and choose the “Email” option.
• Now, click the “Invoice” tab.
• Check the message and deliver it.

Note: In case the link is still disabled, review the online options that are active.

Activate Online Payments in QuickBooks

To enable the Online Payments in QuickBooks, follow these steps:

1. Link the Payments Account

New users need to create an account in QuickBooks Payments. For every company file, only one Payments account can be connected. Here are the steps to connect the payment account:

• In QuickBooks Desktop, head to the “Customers” option.
• Choose the “Link Payment Service to Company File” option.
• Complete the needed credit card protection information.
• Now, click the “OK” button.
• Add the “Payments User ID and Password“.
• Click the “Sign-in” option.
• Select “Connect” to connect or “Transfer” to shift the account.

2. Switch On Online Payments

To switch Online Payments for all clients, follow these steps:

1. Head to the “Edit” option.
2. Now, click the “Preferences” tab and then “Payments“.
3. Choose the ideal payment method.
4. Select the “Apply to Existing Customers” and then click the “OK” button.

To switch Online Payments for all clients, follow these steps:

1. Open the “Customers” segment.
2. Now, click the “Customer Center“.
3. Head to the “Payment Settings” option.
4. Now, click “Online Payments“.
5. Activate the preferred payment options and then click the “OK” button.

4. Adjust the L3 Data Processing Settings

In case the issue continues, modify the L3 settings. Here are the steps to update the L3 settings:

1. Sign in to the Merchant Service Center account.
2. Click the “Account” option and then “Account Profile“.
3. Find L3 Data Processing and click the “Edit” option.
4. Unselect the box and click the “Save” option.
5. Link the data file with the Payments account once more.

5. Confirm and Reconstruct the Data File

A corrupted data file may interrupt the payment links. Here are the steps to verify and recreate the data file:

1. Take a backup of the company file.
2. Access the “Verify Data” tool to spot the damage.
3. Access the “Rebuild Data” utility to fix the file.

Note: These QuickBooks utilities detect file damage and repair it quickly

6. Set the Payment Link on the Invoice

Fix the payment link in case it stays damaged. Here are the steps to set the payment link on the invoice:

1. Open the QuickBooks Desktop.
2. Deselect the Send Email for the invoice and then click the “Save” button.
3. Check “Send Email” twice and then click the “Save” button once more.

7. Install the Latest Windows updates.

QuickBooks often performs imperfectly due to an old Windows version. Here are the steps to update the Windows operating system:

Windows 10:

1. Head to the “Settings” option.
2. Now, click the “Update and Security” option.
3. Now, click the “Windows Update” option.
4. Click the “Check for Updates” option.
5. Download and install updates.

Windows 11:

1. Open the Settings tab.
2. Click the “Windows Update” option.
3. Now, click “Check for Updates“,
4. Choose the option “Download and Install“.

8. Shut down Third-Party Applications

Often, background applications disrupt the QuickBooks operations. Here are the steps to stop third-party programs and prevent disruption of QuickBooks operations:

1. To open the Task Manager, click the “Ctrl + Shift + Esc” keys.
2. Head to the “Processes” tab.
3. Choose unwanted apps and click the “End Task” option.
4. Exit the Task Manager

After the steps are done, the QuickBooks Desktop Payment link not working issue is fixed.

2. QuickBooks Online Payment Link Not Working

To resolve the QuickBooks Online Payment link not working issue, follow these steps:

1. Review the Internet Network

A poor and unreliable internet network can stop invoices from being sent. Here are the steps to check the Internet connection:

1. Use the taskbar or Start menu to open the Control Menu.
2. Choose the option “View network status and tasks“.
3. In the “Connection” segment, choose the network.
4. Check the internet connection and network speed.

A proper internet connection guarantees that the payment link is running properly.

2. Use the Incognito Mode to access QuickBooks Online

Browser cookies and cache often disrupt QuickBooks Online workflow. Here are the steps to access the Incognito mode and prevent cookies and cache interference in different browsers:

Google Chrome:

1. Open the Settings option.
2. Now, click the “Privacy and Security” option.
3. Click the “Third-party cookies” tab.
4. Click the “See all site data and permissions” option.
5. Look for Intuit and erase data.

Safari:

1. Head to the “Preferences” tab.
2. Now, click the “Privacy” tab and choose the “Manage Website Data” option.
3. Reboot the Safari browser.

Firefox:

1. Click the Settings option.
2. Now, click the “Privacy and Security” tab and then choose the “Cookies and Site Data” option.
3. Click the “Manage Data” option.
4. Next, look for “Intuit” and erase all the displayed data.
5. Now, save the changes.

Edge:

1. Head to the “Settings” option.
2. Now, click the “Privacy, Search, and Services” tab.
3. Click the “Cookies” option.
4. Click the option “See all cookies and site data“
5. Look for “Intuit” and erase all displayed.
6. Reboot the Edge browser.

Note: Erasing browser data helps the link to load without issues.

3. Verify the Internet Speed

For a steady business workflow, QuickBooks Online needs a minimum 3Mbps. Here are the steps to review the internet speed:

1. Head to the Google browser and look for “Internet Speed Test“.
2. Perform a speed test and check the outcome.
3. Ensure the speed is no less than 3 Mbps, since poor connections interfere with payment links.

4. Use a Reliable Browser

A reliable browser helps to avoid internal interference with payment links. Here is a link to the different browsers with the minimum versions:

Browser	Minimum Version
Microsoft Edge	79+
Opera	68+
Google Chrome	78+
Mozilla Firefox	76+
Apple Safari	12+
Samsung Internet	10+

5. Check the Payment Link in Invoice Manually

Manual confirmation guarantees the Pay Now link is operational and running. Here are the steps to review the payment link manually:

Simple Text Invoice Message

1. Open QuickBooks Online.
2. Now, choose the “Gear” icon.
3. Now, select the “Accounts and Settings” option.
4. Head to the “Sales” option.
5. Now, click the “Messages” option.
6. Check the “Sales Form” and “Email Message“.
7. Verify that the payment link is displayed in the invoice message.
8. Deliver the invoice.

PDF/HTML Invoice

• Open the “Gear” icon.
• Now, select the “Custom Form Styles“.
• In the “Action” column, click the “Edit” option.
• Head to the “Design” option.
• Now, click the “Change Up the Template” option.
• Choose the “Airy New” template.
• In the “Print Review” section, check the invoice.

Note: Implementing these steps properly restores payment link functionality and helps avoid related issues.

3. Pay Now Link Not Working in QuickBooks Self-Employed

A non-operational QuickBooks payment link stops online invoice payments by customers. This can be fixed with the help of a Merchant Service account and choosing the bank or card payment option while delivering invoices.

Here are the steps to enable QuickBooks payments in QuickBooks Self-Employed:

1. Sign in to QuickBooks Self-Employed.
2. Click the “Invoices” option.
3. Choose the “Create Invoice” option.
4. Find the “Get Paid Fast and Free” option on the new invoice page.
5. Click the option “Set up Payments“.
6. Complete the on-screen guidelines to finish the configuration.
7. After the setup is done, check that the Pay Now link works properly in QuickBooks Self-Employed. This will guarantee seamless online payment for the invoices.

4. Payment Can’t Be Matched or Recorded error

Often, payments cannot be recorded or matched. This occurs due to partially or completely cleared invoices, corrupted payment processes, etc. Consequently, Merchant Service Deposits fail to record payments.

Here are the steps to fix the issue:

1. Invoice cleared or paid partially

1. Find the invoice with the issue.
2. Cancel all payments.
3. Confirm that the complete balance is pending.
4. Close Merchant Service Deposits and open again.
5. Record the payment.

Note: Ensure not to apply payments to emailed invoices manually during online payment.

2. Invoice issued on or before the Closing Date

1. Exit Merchant Service Deposits.
2. Log in as Administrator.
3. Open the “Edit” option and click the “Preferences” option.
4. Now, click the “Accounting” option and then the “Company Preferences” tab.
5. Now, click the “Set Data/Password” option.
6. Change the closing date.
7. Click the “OK” button.
8. Open Merchant Service Deposits again and record the payment.

3. Damaged Payment Method

1. Open the “List” option.
2. Now, click the “Customers and Vendors Profile Lists” option.
3. Now, click the “Payment Method List“.
4. Confirm the default payment methods.
   • Cash
   • Check
   • American Express
   • Discover
   • MasterCard
   • Visa
   • Debit Card
   • E-Check
   • Gift Card
5. Rectify any wrong entry.
6. Add the merchant service deposits again

4. Corrupted ‘Check’ Payment Method

1. Open the Payment Method List.
2. Click twice on the “Check” option.
3. Modify the “Payment Type” to any credit card type.
4. Click the “OK” button.
5. Record the payments once more.

5. Accounts Receivable Problems

1. Corrupted Accounts Receivable
   • Open the “Lists“.
   • Now, click the “Chart of Accounts” option.
   • Add a name to it, for instance, Accounts Receivable 2.
   • Save and close it.
   • Change the present account and modify the name to “Accounts Receivable 2“.
   • Combine accounts when notified.
   • Change the name of the merged account.
   • Now open “Merchant Service Deposits” and then add the payment.
2. Several Accounts Receivable Accounts
   • Combine all the Accounts Receivable accounts.
   • Do not modify the account type of A/P or A/R.
3. Invoice related to sub-accounts
   • Open the “Chart of Accounts“.
   • Choose the invoice displaying the issue.
   • Confirm the linked Accounts Receivable account.
   • Reallocate to the right parent account.
   • Save and close.

5. Merchant Service Deposit Link Not Working

Often, the QuickBooks Merchant Service Deposit link fails to open the deposit screen. Here are the steps to resolve the Merchant Service link not working error:

1. Update QuickBooks to its latest version

1. Update QuickBooks Desktop to its latest version.
2. Verify if the Merchant Service Desktop link fails to function.

2. Remove the Merchant Service Account and reconnect it

1. Open the “Edit” option.
2. Now, click the “Preferences” option and then click the “Payments” tab.
3. Remove the Merchant Service Account.
4. Complete the on-screen guidelines to finish the process.
5. Connect the account once more.
6. Check if the link is operational. In case it does not, deactivate automatic matching and recording of payments manually.

3. Deactivate Automatic Transaction Matching

1. Open “Banking“.
2. Now, click the “Change Your Deposit Settings“.
3. Disable Auto match and record.
4. Choose the “Save” options.

4. Manually link and record payments

1. Click the “Banking” tab.
2. Now, click the “Record Merchant Service Deposits” option.
3. Choose the “Add Payments to Record” option.
4. Click the arrow beside the first deposit.
5. Review all payments.
6. In the Action column, Select the “Add Payments” option.
7. Confirm that the deposit total and the bank statement are the same.
8. Choose the “Save and Close” tab.
9. Review all the bank deposits on the list.
10. Choose the “Record Deposit” option after including every payment.

6. Unrecoverable Error While Loading Record Merchant Service Deposits

This error is often triggered due to a corrupted QuickBooks Desktop software. In some cases, a corrupted company data file triggers this unrecoverable error.

To resolve this issue, follow the steps shared below:

1. Allocate Complete Admin Rights

1. Log in at the merchantcenter.intuit.com.
2. Head to the “Accounts” option.
3. Now, click the “Users” option.
4. Allocate complete admin rights to the particular user.
5. Enter Merchant Service Deposits again.

2. Review Other Workstations

1. Verify the merchant account is not active on multiple devices.
2. Log out from other devices if required.
3. Ensure deposits function properly.

3. Repair Data Damage

1. Review the company file corruption using QuickBooks tools.
2. Fix any damage identified.
3. Try to record deposits once more.

4. Remove and Reinstall QuickBooks Desktop

1. Uninstall QuickBooks Desktop properly.
2. Conduct a complete installation.
3. Connect the merchant account again.
4. Confirm merchant deposits record properly.

In this guide, common QuickBooks Payments Issues related to the Merchant Service have been shared. Readers need to go through each step and implement them in the given order for complete resolution.

In case the issue still persists, feel free to reach out to our QuickBooks professionals. Our support team of QuickBooks professionals and experts is here to help you with such technical issues.

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Frequently Asked Questions