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Fix payroll errors in QuickBooks Online Standard Payroll

SOLVEDby QuickBooks23Updated June 01, 2023

If you're running a business, you need to make sure that your payroll is in order. But even if you're careful, mistakes can happen. In this article, we'll show you how to fix common payroll errors. With our tips, you can keep your business running smoothly

Here are a few reasons why SMP might not be calculating correctly:

  • The employee isn't earning enough to qualify for SMP.
  • The employee hasn't worked for the employer continuously for at least 26 weeks continuing into the 'qualifying week'–the 15th week before the expected week of childbirth.
  • Standard Payroll only calculates on full weeks. For example, if an employee starts their maternity leave in the middle of the week, the first few days of that week are pushed to the next week's period.
  • The pay date is within the pay period. HMRC will assume it's the end date of the period. To calculate an employee's statutory pay, use the HMRC calculator.

Let's explore some reasons why this might be happening and how you can fix it.

  • Make sure you’re using the correct Government Gateway sign in details.
  • National Insurance on the Lower Earnings Limit (LEL) is above Standard Payroll’s maximum threshold. See the full list of rates and allowances HMRC's website.
  • If you have a new employee, and the starter declaration section has been left blank in the Taxes section of the employee’s record in QuickBooks. 
  • Check you have no incorrect National Insurance letter changes. This includes any NI changes made for directors in the middle of the tax year.
    • NI letter changes in the middle of the tax year are supported for regular employees only, not company directors.
    • NI letter B is only applicable to women and will require proof before it is applied.
    • For company directors with an NI letter change mid-tax year, you can update your info in Advanced Payroll. Alternatively, you can keep using the old letter in Standard Payroll and change it at the beginning of the new tax year. Regardless of which method you choose, you will need to let HMRC know about the changes.
  • Make sure that the Account Office (AO) reference and Small Employers Relief are both saved in your settings. If these aren't saved, the FPS won't submit.
  • You have a pay type addition with a negative value. This can lead to a negative year-to-date total, which the FPS won't allow. Try removing the pay type addition with the minus value. If that doesn't work, you can contact HMRC directly for help.

If you are unable to submit your Employer Payment Summary (EPS) to HMRC, there are a few things you can try.

  • Make sure you're using the correct Government Gateway sign in details in your Payroll settings.
  • The submission window is open from the 6th of the current month to the 19th of the following tax month. If you miss the submission window, don't worry–you can always submit an EPS for the following month.
  • Make sure you select Small Employer Relief when you've included reclaimable statutory payments on your pay run.

However, there are certain circumstances in which you won't be able to send an EPS to HMRC. For example, if you're claiming the employer allowance or reclaiming statutory payments, you won't be able to submit an EPS. Similarly, if you're stopping a PAYE scheme, you also won't be able to submit an EPS.

If you're a business owner using QuickBooks Online, you may be able to claim Employment Allowance. To claim employment allowance, you only need to send an EPS to HMRC once. This can be at the beginning of the tax year or at any time during the tax year. Once you've made a claim, the EPS will be ready on the 6th of every tax month in QuickBooks. It will include your eligibility.

If you accidentally delete the EPS submission, don't worry. You can recreate it by rolling back the pay run to the start of the tax year and deleting each payroll chronologically.

To recreate the EPS:

  1. Go to Settings ⚙, and then Account and settings
  2. In Payroll, select Employer NI relief.
  3. Change employment allowance to ‘No, I don’t qualify’ and Save.
  4. Go back to Payroll settings, and change employment allowance to ‘Yes, I qualify’, and then Save.

This will recreate the EPS submission and allow you to make a submission to HMRC. You can see the status of all your EPS submissions by going to the Taxes section, and then Payroll Tax.

You need to submit an EPS to HMRC in order to claim statutory payments like maternity or paternity pay. This needs to be done during the same tax period that the SMP/SPP is in during the pay run.

If you don't see the option to send an EPS to HMRC, check the following:

  • The ‘Small employers relief’ and ‘Employment Allowance’ fields are empty in your Payroll settings. Fill in the fields with either Yes or No to generate an EPS.
  • Statutory payments are recorded as additional payments. You'll need to enter the Statutory payment into the employee’s record. To do this, go to:
    1. The employee's profile.
    2. Select Actions.
    3. In the Employees Leave section, choose the relevant statutory payment.

If you need to stop a PAYE scheme, the best course of action is to speak to your accountant or HMRC directly. Unfortunately, you can't end a PAYE scheme by sending an EPS.

If you try to delete week 12 or week 52 or 53 of the last tax year, you may see the error message "Something went wrong when rolling back a pay run.". To fix this, you need to make sure that you're only trying to delete pay runs from the current tax year.

This error can also happen if you've recently made changes to your payroll, like if you add a new employee or create a new pension scheme. To fix this, delete the new employees before deleting the pay run. Once you've made changes to the final period of the final tax year, you can add the employees back in QuickBooks.

If you’ve created a new pension scheme, try deleting it and then roll back the pay run. If you’re still having trouble doing this, reach out to Support for help.

You may have come across the dreaded "employee set up" error. This can be a frustrating problem, but fortunately, there are a few things you can do to fix it.

  • If your employee has a custom pension set up, make sure you choose the correct taxation method in the pensions settings. 
  • You may have entered an unsupported National Insurance letter change, like changing C to J. 
  • Check that the NI letter in the employee’s details matches the code in their Pay History, Tax and NI details section in QuickBooks. 
  • If you’re setting up a new employee in the middle of the tax year, make sure you enter 0 in the Pay History section. 

See how to edit employees in QuickBooks.

If you're seeing the error message "An error has occurred with the auto enrolment of this employee," don't worry–there are some steps you can take to fix it.

  • Check that the employee's date of birth and gender are entered correctly in their records. The employee's age should be over 16 years old and below 74. 
  • Make sure that the employee meets the eligibility criteria for auto-enrolment.
  • If the employee has been postponed from auto enrolment, enrol the employee when prompted and enter 0 in the contributions field within the employee's settings.
  • If the employee has opted out of auto enrolment, you won’t be able to opt them back in until the next re-enrolment period.  

See workplace pensions

There are a few things that can cause errors when creating journals in Standard Payroll. Here are some troubleshooting tips if you can’t create journal entries. 

1. Make sure that the 'Close the books' period doesn't cover the same period you're trying to create the journal entry for

To check this:

  1. Select the gear icon
  2. Select Account and settings, and then Advanced
  3. Next to Accounting, select the pencil icon.
  4. Use the toggle to switch off Close the books.

2. Check that the ‘Net pay account’ isn’t mapped in a foreign currency

To check this: 

  1. Select the gear icon.
  2. Select Account and Settings, and then Advanced.
  3. In the Currency section, set the home currency to British Pound Sterling.

3. Check to see if your payroll liabilities and expenses sub-accounts are arranged correctly

There should be three sub-accounts beneath both your Payroll liabilities and Payroll expenses account. If these accounts are out of order, it can cause problems with your journal. To fix this: 

  1. Change the name of the main payroll accounts, Payroll liabilities and Payroll expenses, to have to word ‘old’ at the end and then Save.
  2. Try running a new payroll. This will create a new set of payroll liabilities and expenses accounts, which should also force the created of the correct payroll journals. If that doesn’t work, you may need to roll back and re-run payroll. 
  3. Double check that the changes you've made have been registered by refreshing the audit log. To do this, go to your Account and settings and then select Audit Log under Tools.

4. Switch off the ‘Warn when a duplicate journal number is used’ setting

To do this: 

  1. Select the gear icon.
  2. Select Account and settings, and then Advanced.
  3. In Other preferences, turn off Warn if duplicate journal entry number is used.

If you see the error message "Missing required fields on a pay run" when trying to process a pay run in Standard Payroll, don't worry–there's an easy fix.

There are two possible reasons for this error: either you have too many employees, or one (or more) of your employees is missing some required information. To fix it, go back and fill in the missing information. If you have too many employees, the easiest solution is to split them into multiple pay runs.

This error message can mean that there is a reclaimable statutory payment on the pay run, but nothing has been selected in the Small Employer's Relief (SER) status in payroll settings. To fix this, go to your payroll settings and select the appropriate SER status. This will help ensure that all statutory payments are correctly calculated and accounted for.

If you're still seeing the error message after filling in all the mandatory fields, it's possible this may be a browser/network issue. See Clear cache and cookies to fix issues when using QuickBooks

This error is usually caused by a browser or network issue, but clearing your cache and cookies should do the trick. If that doesn't work, reach out to QuickBooks Support and we'll be happy to help.

If you see the message 'Something went wrong. Please wait a moment and try again. If the problem continues, contact us.', try checking the following in your QuickBooks:

  • Make sure you’re using the correct Accounts Office (AO) reference. 
  • You are using the correct PAYE reference.
  • Your Government Gateway user ID and password is correct–make sure there is no space before or after when entering your details.

If all the details are correct and you still see the error message, try resetting your Government Gateway password. This should be at least 12 characters long and shouldn't include ampersands (&) and pound signs (£).

Payroll error codes

Are you having trouble with your payroll? If you're seeing error codes, don't worry–you're not alone. We'll cover some of the most common payroll error codes and how to fix them.

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