How to Submit an FPS in QuickBooks

At Towerstone Accountants we provide specialist limited company accountancy services for directors and owner managed businesses across the UK. We created this webpage for business owners who want practical guidance on choosing and using accounting software, including day to day bookkeeping tasks, invoicing, bank feeds, and reporting. Our aim is to help you keep accurate records, reduce admin time, and stay compliant with HMRC and Companies House requirements.

Submitting an FPS is one of the most important payroll tasks a UK business has to complete and it is also one of the most commonly misunderstood. In my experience problems with FPS submissions rarely come from deliberate non compliance. They usually come from uncertainty about timing confusion about what an FPS actually is or assumptions that payroll software submits things automatically without any action required.

If you run payroll through QuickBooks you are responsible for ensuring that an FPS is submitted correctly and on time every time employees or directors are paid. Getting this right keeps you compliant with HMRC avoids penalties and ensures that employees’ tax and National Insurance records are accurate.

In this guide I will explain clearly what an FPS is when it must be submitted how QuickBooks handles FPS submissions and the exact step by step process to follow. I will also cover common mistakes I see in practice and how to fix issues if something goes wrong.

What an FPS actually is

FPS stands for Full Payment Submission.

It is a payroll report that tells HMRC about payments made to employees or directors and the tax and National Insurance deductions associated with those payments.

An FPS includes details such as

• Employee pay
• Income Tax deducted
• Employee National Insurance
• Employer National Insurance
• Student loan deductions if applicable
• Statutory payments

The FPS is submitted every time you pay someone through payroll.

Why FPS submissions matter

The FPS is how HMRC keeps track of PAYE in real time. It updates each employee’s tax record and ensures that PAYE liabilities are calculated correctly.

If an FPS is not submitted

• HMRC may think no pay has been made
• Employees’ tax records may be incorrect
• PAYE liabilities may be miscalculated
• Penalties and notices may be issued

Submitting the FPS accurately and on time is a legal obligation.

When an FPS must be submitted

The key rule is simple but often overlooked.

An FPS must be submitted on or before the date you pay your employees.

Not after. Not at the end of the month. Not when it is convenient.

If you pay someone on 25th of the month the FPS must reach HMRC on or before the 25th.

Late submissions are one of the most common payroll compliance failures.

Who needs to submit an FPS

Any business that runs payroll and pays employees or directors must submit an FPS.

This includes

• Limited companies paying directors
• Companies with employees
• Small companies with one person on payroll
• Businesses paying monthly quarterly or irregularly

Even if you only pay yourself as a director once a month an FPS is still required.

What QuickBooks does in the FPS process

QuickBooks payroll software is designed to

• Calculate pay and deductions
• Prepare the FPS data
• Submit the FPS electronically to HMRC

However it does not decide when payroll is finalised. You must still run payroll and submit the FPS.

QuickBooks supports FPS submission but it does not remove responsibility.

What you need before submitting an FPS in QuickBooks

Before you can submit an FPS through QuickBooks you need

• An active payroll setup in QuickBooks
• Correct employee or director details
• Correct PAYE reference numbers
• A Government Gateway connection to HMRC

Without these in place FPS submission will fail.

Connecting QuickBooks to HMRC

Before your first FPS you must authorise QuickBooks to communicate with HM Revenue and Customs.

This involves

• Entering your Government Gateway credentials
• Granting permission for payroll submissions
• Confirming PAYE scheme details

This is usually done during payroll setup but should be checked if submissions fail.

Step one log into QuickBooks

Start by logging into your QuickBooks account.

Once logged in

• Select the correct company
• Go to the Payroll section
• Choose the relevant pay run

Make sure you are working in the correct pay period.

Step two review the payroll period

Before submitting an FPS you must run payroll for the correct period.

Check

• Pay period dates
• Pay frequency monthly or weekly
• Payment date
• Employees included in the run

The payment date is critical because it determines the FPS deadline.

Step three check employee details

Incorrect employee details are a common cause of FPS errors.

Before submitting check that each employee has

• Correct name
• Correct National Insurance number
• Correct date of birth
• Correct tax code

For directors ensure director status is set correctly within QuickBooks.

Step four review pay and deductions

Once payroll is calculated review the figures carefully.

Check

• Gross pay
• Income Tax
• Employee National Insurance
• Employer National Insurance
• Any pension or student loan deductions

QuickBooks calculates these automatically but errors in setup can lead to incorrect results.

Step five finalise the payroll run

In QuickBooks payroll must be finalised before submission.

Finalising the payroll

• Locks the figures
• Confirms the payment date
• Triggers the FPS submission process

Once finalised changes usually require a correction rather than a simple edit.

Step six submit the FPS to HMRC

After finalising payroll QuickBooks will prompt you to submit the FPS.

This is usually a clear action such as

• Submit payroll to HMRC
• Send FPS

When you confirm this QuickBooks sends the FPS electronically to HMRC.

You should wait for confirmation that the submission was successful.

Step seven confirm FPS submission status

QuickBooks will display a submission status.

You should see confirmation that

• The FPS was sent
• HMRC received the submission
• No errors were reported

Always check this status. Do not assume submission has succeeded.

What happens after the FPS is submitted

Once the FPS is accepted

• HMRC updates employee tax records
• PAYE liabilities are calculated
• Your PAYE account is updated

You can then proceed to pay employees knowing that payroll has been reported correctly.

Submitting an FPS for directors only payroll

Many small companies only have directors on payroll.

The FPS process is the same.

Key points for directors

• Directors must still be reported through FPS
• Annual earnings periods apply
• FPS submission is still required on payment

Even if no tax is deducted an FPS must be submitted.

FPS submission with zero pay

There are situations where no one is paid in a period.

If no payments are made

• An FPS is usually not required for that period
• However you may need to submit an EPS instead

QuickBooks will guide you depending on circumstances.

What an EPS is and how it differs

EPS stands for Employer Payment Summary.

It is used to report things such as

• No payments made in a period
• Statutory pay recovered
• Apprenticeship Levy
• Employment Allowance

Do not confuse FPS and EPS. They serve different purposes.

Common FPS submission errors in QuickBooks

In practice I see the same errors repeatedly.

These include

• Submitting the FPS after pay day
• Incorrect payment dates
• Missing National Insurance numbers
• Government Gateway connection expired
• Duplicate payroll runs

Most errors can be corrected but prevention is easier.

What to do if an FPS is submitted late

If an FPS is submitted late

• HMRC may issue a late filing notice
• Penalties may apply if lateness is persistent

If it is a one off error it is often best to submit as soon as possible and keep records explaining why.

Correcting an FPS submitted with errors

If an FPS is submitted with incorrect figures

• Do not submit a second FPS for the same pay run
• Instead submit a correction through QuickBooks

QuickBooks allows you to

• Run an amended payroll
• Submit corrected figures to HMRC

The correction process must be followed carefully.

Submitting FPS for irregular payments

If you pay employees irregularly

• FPS is still required each time payment is made
• There is no exemption for irregular pay

This includes one off bonuses or director payments.

FPS submission for new starters

When a new employee or director is paid for the first time

• Their details are included in the FPS
• Starter information is reported to HMRC

Ensure starter details are entered correctly before running payroll.

FPS submission for leavers

When an employee leaves

• Final pay is reported through FPS
• Leaving date is included

QuickBooks handles this within the payroll process but details must be accurate.

How to check FPS history in QuickBooks

QuickBooks keeps a record of payroll submissions.

You can review

• Past payroll runs
• FPS submission dates
• Submission status

This is useful if HMRC query whether an FPS was sent.

Record keeping for FPS submissions

Good records protect you if there are queries.

You should retain

• Payroll reports
• FPS submission confirmations
• Payment records
• Correspondence with HMRC

QuickBooks stores much of this automatically but it is still your responsibility.

How FPS submissions affect PAYE payments

FPS submissions determine how much PAYE and National Insurance you owe.

The amounts shown in your PAYE account are based on

• FPS data submitted
• EPS adjustments where applicable

If FPS data is wrong PAYE liabilities will also be wrong.

Deadlines for paying PAYE after FPS submission

Submitting an FPS does not pay HMRC.

You must still pay

• PAYE
• Employee National Insurance
• Employer National Insurance

By the relevant monthly or quarterly deadline.

FPS submission and PAYE payment are linked but separate obligations.

Using an accountant with QuickBooks payroll

If you use an accountant clarify

• Who runs payroll
• Who submits FPS
• Who monitors deadlines

Assuming someone else is submitting the FPS is a common cause of missed filings.

Director only companies and FPS mistakes

In one director companies FPS errors are particularly common.

Typical issues include

• Paying directors but forgetting to run payroll
• Paying monthly but submitting FPS quarterly
• Thinking dividends remove the need for FPS

Any salary paid to a director must go through FPS.

FPS submission and Real Time Information compliance

FPS submissions are part of the Real Time Information system.

HMRC uses RTI to

• Monitor PAYE in real time
• Identify late or missing submissions
• Calculate benefits and entitlements

Consistent FPS submission keeps your PAYE record clean.

What HMRC expect to see

From HMRC’s perspective correct FPS submission means

• On or before pay day
• Accurate figures
• Consistent reporting

Repeated errors or late submissions increase scrutiny.

Troubleshooting FPS issues in QuickBooks

If FPS submission fails in QuickBooks

• Check Government Gateway connection
• Check PAYE reference numbers
• Review error messages carefully
• Re authorise the HMRC connection if needed

Most issues are technical rather than fundamental.

When to seek help

You should seek help if

• FPS submissions repeatedly fail
• PAYE figures do not match expectations
• HMRC issue penalty notices
• Payroll setup is unclear

Fixing payroll issues early avoids escalation.

Best practice for FPS submissions in QuickBooks

From experience the most reliable approach is

• Run payroll on a set schedule
• Submit FPS immediately after finalising payroll
• Double check submission confirmation
• Keep payroll simple where possible

Consistency reduces mistakes.

Final thoughts from experience

Submitting an FPS in QuickBooks is not difficult but it is critical. The software makes the process straightforward but it does not remove responsibility or judgement.

In my experience payroll problems are rarely about complex calculations. They are about timing assumptions and missed clicks. Once you understand that the FPS must be submitted on or before pay day and you build that into your routine the process becomes predictable and stress free.

QuickBooks is a capable payroll tool when set up correctly. Used with care it keeps you compliant supports your PAYE obligations and avoids unnecessary penalties. The key is treating FPS submission as a core business process rather than an afterthought.

You may also find our guidance on does quickbooks do payroll and what is quickbooks helpful when exploring related accounting software tasks. For a broader overview of software options and setup guidance, you can visit our accounting software hub.