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QuickBooks Tax Payment was Rejected? Here’s What To Do Now

• 
• By Jonathan Browns
• Feb 17, 2026
• Taxation
• 7 min read

Wondering why your QuickBooks Tax Payment was rejected? It may happen for several reasons, including invalid bank details, incorrect agency setup, or an expired EFTPS password. So, to fix this issue, you are advised to look for the cause of the issue, void the rejected payment, and then resubmit it.

In this blog, we have explained the detailed steps to resubmit a rejected tax payment in QuickBooks Desktop and Online. We have also described why a rejected e-payment or e-filed tax form occurs and how to fix it.

Thinking about what to do if the QuickBooks tax payment was rejected? Directly Call Us : +1-866-408-0444 and connect with our QB professionals to get instant help.

Reasons Why Your E-Filed Tax Form or E-Pay Tax Payment Was Rejected

If you have got any message in QuickBooks or a notice via IRS or state agency regarding rejected e-payment or e-filed tax form, then you’re not alone. Below, we have described all the reasons why tax payments get rejected in QuickBooks, how to fix and resend the tax payment or form.

1. Duplicate Tax Filing-

Duplicate tax filing indicates that the IRS or state agency has two tax forms with your information for the same period. This situation usually occurs when you have accessed multiple payroll providers in the same quarter and forgot to cancel one.

a. QuickBooks Online Payroll

You must connect with the IRS or state agency immediately and work with them to check whether they have accepted one form or rejected both of them. So, it’s essential to connect with QuickBooks to check whether they can help you fix your forms.

Read More:- QuickBooks Online Payroll

b. QuickBooks Desktop Payroll Enhanced

Connect with the IRS or state agency to find out if they have accepted one form or rejected both of them. Then, as part of the situation, you have to file an amendment or resend the form via the agency.

2. Invalid or Incorrect Account Number

It simply states that either your Federal Employer Identification Number (EIN) or state account numbers are incorrect in QuickBooks, and it doesn’t tally with the one that the agency filed for your business.

a. QuickBooks Online Payroll

• Connect with the IRS or state agency to find out the correct EIN or state account number.
• You can also connect with QuickBooks to update your EIN or state account number in the software.
• In case your tax form is rejected, move to the Payroll Overview page and verify the To Do List for further steps.

• If your tax payment was rejected, connect with the IRS or state agency to transfer the payment to the correct account number.

b. QuickBooks Desktop Payroll Enhanced

• You have to update your EIN or state account number.
• If your tax form was rejected, you must resend your payroll tax form.
• Alternatively, you can also connect with the IRS or state agency for transferring payments to the right account number.

3. The form was sent too early

There are some agencies that don’t accept early filings or payments, especially at the time of e-filing or e-paying before the filing period ends. So, at that time, you must resend your filings or payment closer to the due date.

4. The tax deposit or filing schedule is correct

It states that your state tax deposit schedule, IRS, or the filing schedule has been changed by your agency, and the payment or form was sent at the wrong time.

a. QuickBooks Online Payroll

• Directly connect with the IRS or state agency to receive the correct schedule and form. Also, you need to check whether there are any additional payments that you need to make.
• You are required to update the payment or filing schedule in QuickBooks.
• If mandatory, send the correct form or payment.

b. QuickBooks Desktop Payroll Enhanced

• Directly consult with the IRS or the state agency to receive the correct schedule or form. Also, check for any additional payments to be made.
• Next, update the federal or state payment or filing schedule in QuickBooks.
• When required, you must send the accurate federal or state form or payment.

What are the common rejection reasons for QuickBooks Desktop Payroll Enhanced Only?

Below, we have explained all the reasons and understand how to resubmit a rejected tax payment in QuickBooks Desktop Payroll Enhanced only.

1. Federal E-Pay PIN is incorrect

This issue may occur when you have recently updated your bank account for e-payments on the EFTPS website, and the same isn’t updated on QuickBooks. So, to fix the issue, you must update the PIN using these steps.

• Move to Employees > Payroll Center > Pay Liabilities tab.

• Now, choose your federal tax, and click View/Pay > E-payment > E-Pay option.
• Next, make sure that the checkbox of “Remember My Information for Next Time” remains unmarked.
• Provide your new 4-digit PIN along with the EFTPS Internet Password.
• You also have to provide the other missing details.
• Finally, hit the Submit option to complete.

Re-enter the 4-Digit PIN and EFTPS internet password the next time you make the e-payment. Then, tap on the Remember My Information for Next Time to restore the new details.

If you don’t know your PIN, directly connect with the IRS.

• IRS eftps (e-pay) help desk: 800-555-4477
• IRS e-file help desk: 866-255-0654

2. Federal e-file PIN is incorrect

If an incorrect e-file PIN is entered, your e-file will be rejected. You must try to remove it and then re-enter the PIN.

• Move to the Employees > Payroll Tax Forms and W-2 > Process Payroll Forms.
• Choose the federal form that you want to file and click Create Form. You have to pick the form filing period and then hit OK.
• Now, start checking every part of the form. Alternatively, you can also choose the Check for errors and then do the required changes.
• Head to the Submit Form > E-file option.
• Unmark the checkbox of Remember My Information for Next Time.

• Next, provide the 10-digit IRS e-file PIN and check that it’s entered properly.
• Finally, choose the Remember My Information for Next Time to save the new information.

If you don’t know your PIN, then contact the IRS.

• IRS eftps (e-pay) help desk: 800-555-4477
• IRS e-file help desk: 866-255-0654

3. Internet Password (for e-pay) expired

You may require an internet password for EFTPS, which is a 12-30 character password used to log in to the EFTPS.gov website. You must change the EFTPS Internet Password and then resend the e-payment or e-filing.

How to Edit Payroll Tax Payment in QuickBooks Online?

Perform the following steps to edit a payroll tax payment in QuickBooks Online, depending on whether the payment is recorded manually or electronically.

Method 1: Edit Manually Recorded Tax Payments

If you record the tax payment (outside of QuickBooks) and need to change the amount or date, do as follows:

• Move to Payroll > Payroll Tax > Payments tab > Record tax payments (prior tax history).
• After this, select the date range to get the payment and click Details > Edit payment.
• Now, edit the tax payment and hit Update payment.

Method 2: Edit or Delete Scheduled/Automatic Payments

If QuickBooks is previously set to automatically pay taxes and you need to make certain changes, you can delete them if they have not processed.

• Choose the Taxes > Payroll Tax > Payment History option.
• After this, pick the tax payment that you want to edit and hit the Edit drop-down arrow. Then, tap on Delete.

Learn More:- QuickBooks GoPayment App

Method 3: Correcting Errors after filing

If your tax payment has been previously processed and the filing is done, perform the following actions.

• For Underpayments- You must generate a new tax payment for the remaining amount owed.
• For Overpayments- Switch to the Payments tab, choose the overpaid tax, and click Resolve to get a refund or apply the credit for future payments.
• For Incorrect Amounts (No Edit Option)- If you aren’t able to edit the payment, delete it and correct the underlying paychecks from the Paycheck list. Then, you must recreate the payment.

Read More:- Set Up Credit Card Processing in QuickBooks Online

How to Correct the Rejected Tax Payment in QuickBooks?

Whenever a tax payment you try to e-pay is rejected by the IRS or a state agency, QuickBooks shows the reject status along with the reason for rejection. However, to fix and resubmit it, perform these steps.

Step 1: Determine the Reason Why It Was Rejected

The first step is to know the reason for the rejection. Perform these steps.

• Move to the Employees menu > Payroll Center > Pay Liabilities tab.
• After this, choose the E-Payments option from the Payment History section.
• Now, check for the rejected 941 payment and tap on the Agency Rejected link.

Step 2: Void the Rejected Payment

After knowing the reason for the rejected tax payment in QuickBooks, you can now void the rejected payment.

• Choose the Void rejected E-Payment button.
• Consequently, it will launch the Liability in the Payroll Center.

Step 3: Correct the Issue

Now, the last step is to correct the issue.

• Move to the Pay Liabilities tab from the Payroll Center.
• Choose the Liability that you have recently voided.
• At last, hit the E-payment and then the E-Pay option. Later on, submit the payment once again.

Read more:- QuickBooks Online Payroll Subscription

Ending Words

QuickBooks tax payment was rejected issue may occur while providing the incorrect bank details, expired credentials, or due to data mismatching. However, by understanding the root causes and solutions described in this post, you can easily fix the issue. If you need any help, connect with your BizBooksAdvice experts for quick resolution.

Frequently Asked Questions (FAQ’s):-

Question 1: How to resubmit a rejected tax payment in QuickBooks Desktop?

Ans. Before you resubmit the rejected tax payment in QuickBooks Desktop, first know the reason for rejection, void the rejected tax, and then correct the issue. Follow the steps for resubmission.

• Choose the Pay Liabilities and then the tax liability you voided.
• Hit the E-Payment > E-Pay option.
• Add the correct details and then resubmit the payment.

Question 2: Why are tax payments rejected in QuickBooks?

Ans. The tax payments get rejected in QuickBooks because of incorrect bank account/routing numbers, duplicate filings, expired EFTPS PIN/password, and invalid deposit schedules.

Question 3: How long do I have to fix my rejected tax return?

Ans. If you get the rejection of e-filing of the return by the day after the filing deadline, then the IRS will provide you with a rejection grace period of up to 5 days to refile it timely.

Question 4: How do I record a rejected payment in QuickBooks?

Ans. To record the rejected Payment in QuickBooks.

• Move to All Apps and look for the bounced Check or returned payment.
• Choose the transaction to get more details and pick the customer whose payment has bounced.
• Hit the Accounts Receivable option and then the Add.

Question 5: What happens if an IRS payment is rejected?

Ans. If you fail to process the payment, you will obtain a payment return notice via mail, prompting you to resubmit the payment. When any penalty is applied by the IRS, you will get another notice via mail mentioning the penalty amount.

Question 6: What are the common reasons for declined payments?

Ans. The following are the reasons behind the declined payments:

• Incorrect card details
• The card has expired or deactivated
• Accessing an unsupported card type
• If their card is on hold.
• You have crossed the daily limit to make payments.

Question 7: How to delete the rejected tax payment in QuickBooks Desktop?

Ans. To delete the rejected tax payment.

• Reach out to the EFTPS website and click on payments.
• After this, sign in to the EFTPS account.
• Click the Cancel Tax Payment and use the following steps.