Self Assessment Software: FAQ Answered for Payroll Clients
Self assessment software files your personal tax return, while payroll software reports pay to HMRC through RTI, so a driver running a limited company usually needs both. This FAQ explains where each tool starts and stops, how figures flow between them, and what mistakes cost.
Published 3 October 2026 · Updated 3 October 2026
Self assessment software and payroll software are two different tools. Payroll software reports pay and PAYE to HMRC each payday, while self assessment software files your personal tax return, normally once a year. If you run payroll as a limited company director or employer, you will usually need both jobs covered, and some products do both.
This FAQ is for Uber, Bolt and private hire drivers who have moved to a limited company or who employ someone. It answers the questions we hear most often about which tool does what, where the numbers travel between them, and where drivers go wrong. For choosing a product, we point you to our other guides rather than repeating them.
Key takeaways
- Payroll software sends Real Time Information (RTI) reports to HMRC. It does not file your personal Self Assessment return.
- Self assessment software files the return (SA100) and must be on HMRC's list of commercial suppliers to submit it.
- Your director's salary and dividends appear in both worlds, so one set of figures must match across them.
- A few accounting packages combine both jobs, but you still need to check each feature before you rely on it.
- Missing a deadline in either system triggers separate penalties.
What is self assessment software?
Self assessment software is a program or online service that helps you complete and submit your personal tax return to HMRC. It calculates your tax and National Insurance, checks your entries, and files the return electronically. HMRC publishes a list of commercial suppliers whose products can submit valid returns.
Payroll software is a separate category. It records pay, works out PAYE and National Insurance, produces payslips and reports to HMRC. Think of payroll as the weekly or monthly job and the return as the yearly summary.
Can payroll software file my Self Assessment tax return?
Usually no. Standard payroll software only handles employer reporting, such as the Full Payment Submission (FPS) sent on or before each payday. It cannot complete your personal return. Some all-in-one accounting platforms offer both modules, but they are separate features and you must check that the Self Assessment part is included in your plan.
According to HMRC's guidance on payroll software for employers, the software must report PAYE information online unless you are exempt. That guidance covers payroll only. For returns, HMRC keeps a separate list of commercial Self Assessment software suppliers, which HMRC updated on 29 September 2026.
In practice, a driver who owns a limited company has three filing jobs: payroll reports, the company's accounts and Corporation Tax return, and a personal tax return if one is needed. Each has its own deadline and its own route. Treat them as three lanes, not one.
What is the difference between RTI and Self Assessment?
RTI is how employers report pay and deductions to HMRC, usually every time they pay someone. Self Assessment is how an individual reports their total income for a tax year, then pays any tax still due. RTI is per payday and about the employer. Self Assessment is yearly and about you as a person.
A director who pays themselves a small salary through payroll creates RTI reports for that salary. If they also take dividends or have other untaxed income, those may need to go on a Self Assessment return. The two systems meet when HMRC compares the salary you reported through payroll with the employment figures on your return.
| Question | Payroll software | Self assessment software |
|---|---|---|
| Main job | Calculate PAYE and report pay | Calculate your personal tax and file the return |
| Who files | The employer or its agent | You, or your agent |
| How often | Each payday (FPS), plus monthly summaries if needed | Once a year, with 31 January 2027 the online deadline for 2025/26 |
| Needs a limited company | Only if you pay yourself or staff through PAYE | No, sole traders use it too |
| Typical figures | Gross pay, tax, NIC, pension | Salary, dividends, profits, reliefs, tax due |
| Official list | HMRC recognised payroll software | HMRC commercial Self Assessment suppliers |
Do I need self assessment software if I run payroll for my own company?
Not always, but often. Many directors only take a salary through payroll and never need a return. Others do, for example when they take dividends above the tax-free allowance, have rental income, or have other income not taxed at source. Check the current rules on GOV.UK before assuming either way.
GOV.UK's page on who must send a tax return lists the usual triggers, such as self-employment above £1,000, untaxed income and Capital Gains Tax. HMRC's dividend tax page shows a £500 dividend allowance for 2026/27, with rates of 10.75%, 35.75% and 39.35% above it.
Why dividends often decide the answer
Payroll software knows about salary, not dividends. Dividends are paid by the company from profits, and the tax on them is not collected through PAYE. That is why directors who take dividends so often end up on Self Assessment, even when payroll is running perfectly.
Which software do I need for each job?
Match the tool to the job. For pay, you need payroll software that is recognised by HMRC. For the yearly personal return, you need Self Assessment software from HMRC's list, or the free online return. For company accounts and Corporation Tax, you need separate accounting tools. Some packages bundle more than one.
To compare products and what Making Tax Digital changes, read our guide to self assessment software and Making Tax Digital. For a walk-through of filing a personal return in software, see how to use self assessment software for personal tax. We avoid repeating those here.
Free payroll options
HMRC offers free payroll software called Basic PAYE Tools for businesses with fewer than 10 employees. According to HMRC's Basic PAYE Tools page, you must be registered as an employer with PAYE Online access. HMRC says the tool is not designed for agents or bookkeepers, and it works on Windows, macOS and Linux with an internet connection.
Paid and bundled options
Paid products add payslip templates, pension submissions, holiday pay tools and multiple pay frequencies. HMRC's payroll software page warns that some packages lack features such as the Employer Payment Summary (EPS) or Earlier Year Update. Check this before you buy, because a gap here can cost you time at year end.
How do I move salary and dividend figures between payroll and my return?
Take your totals from your payroll records after the tax year ends on 5 April, then enter them on your return. Use the figures on your P60 for employment pay and tax. Enter dividends from your board minutes and dividend vouchers. The numbers must agree with what the company reported through payroll.
- Download your final payroll summary and P60 after the last payday of the tax year.
- Confirm that the pay and tax figures match what your payroll software reported through RTI.
- List every dividend paid in the tax year, with dates and amounts, from your company records.
- Gather other income, such as rental profit, interest and any self-employed profit.
- Open your self assessment software and complete the employment, dividend and other income pages.
- Compare the calculated tax with your payroll tax and expected dividend tax, and investigate any large gap.
- Submit before the deadline and record the payment due on 31 January.
This step is where most mismatches arise. A salary typed in wrongly, a dividend entered in the wrong year, or a month missed from payroll can lead to a letter from HMRC. A reconciliation takes minutes, while correcting later takes much longer.
How do deadlines compare across payroll and Self Assessment?
Payroll deadlines repeat during the year, while Self Assessment has fixed annual dates. For payroll, you send an FPS on or before each payday and pay HMRC by the 22nd of the following tax month if paying electronically. For the 2025/26 return, the online filing and payment deadline is 11:59pm on 31 January 2027.
These dates come from HMRC's running payroll guidance and its Self Assessment deadlines page. The same deadlines page says paper returns are due by 31 October 2026, and returns paid through your tax code are due by 30 December 2026. For a wider calendar, use our key tax dates for Uber drivers.
What are the penalties if I miss a payroll or Self Assessment deadline?
Both systems charge penalties, and they are separate. For Self Assessment, HMRC states an initial £100 late filing penalty, then £10 a day after three months up to £900, then further charges after six and twelve months. Late payment adds charges of 5% of the unpaid tax at 30 days, six months and twelve months, plus interest.
Late payroll reports and payments also carry penalties, but the amounts depend on the number of employees and how often you are late. We do not quote a figure here. Check the current penalty rates on GOV.UK, as the Self Assessment penalty figures above cover the personal side only.
Does Making Tax Digital change which software I need?
It might, if your self-employed or rental income passes the qualifying threshold. Making Tax Digital (MTD) for Income Tax starts for qualifying income above £50,000 from 6 April 2026, then £30,000 from 2027 and £20,000 from 2028. Director's salary and dividends are not the same as self-employed income, so check your own position on GOV.UK.
HMRC's guidance on using Making Tax Digital for Income Tax explains how the new way to do Self Assessment works for sole traders and landlords. If you also drive as a sole trader alongside your company, read our comparison of Self Assessment and Making Tax Digital.
What is a worked example of payroll and Self Assessment together?
The example below shows how one limited company director's figures flow from payroll into the return. It is an illustration, so do not treat the numbers as advice for your own case.
Illustrative example: Priya is an invented driver who runs her own limited company. In 2026/27 the company pays her a salary of £12,570 through payroll and she takes £20,000 in dividends. She has no other income.
| Item | Where it is reported | Amount |
|---|---|---|
| Salary | Payroll software (RTI), then the return | £12,570 |
| Dividends | Company records, then the return | £20,000 |
| Dividend allowance | Return calculation | £500 |
| Dividends taxable at 10.75% (assuming basic rate) | Return calculation | £19,500 |
| Dividend tax before other reliefs | Return calculation | £2,096.25 |
In this illustration, 10.75% of £19,500 is £2,096.25. The payroll software would show no PAYE tax on the salary, so the payroll data alone gives an incomplete picture. Only the return, filed with self assessment software or on HMRC's own service, brings the dividend tax into view. Your own result depends on your total income and the rates and allowances for your tax year.
What are the common mistakes and the penalty each triggers?
Most problems come from treating payroll and the return as one task, so the two filings drift apart. Each mistake below has a typical consequence, and a short yearly checklist will help you avoid all of them.
- Assuming payroll software files your return. Consequence: a missed deadline and the £100 late filing penalty, plus daily charges after three months.
- Using unrecognised or out-of-date software. Consequence: rejected submissions and a late filing. Check the HMRC list before you pay for a product.
- Entering dividends in the wrong tax year. Consequence: wrong tax calculation, then interest and possible penalties for an inaccurate return.
- Not paying the tax due by 31 January. Consequence: late payment charges of 5% at 30 days, six months and twelve months, plus interest.
- Letting payroll lapse after a quiet month. Consequence: late payroll reporting, with penalties that depend on your circumstances; check GOV.UK for the current rates.
- Changing payroll provider without checking Payroll IDs. Consequence: duplicated records and wrong PAYE figures, as HMRC's payroll software guidance warns.
Key terms
- RTI (Real Time Information): the system employers use to report pay and deductions to HMRC.
- FPS (Full Payment Submission): the report sent on or before each payday.
- EPS (Employer Payment Summary): a monthly report used for adjustments or when no one was paid.
- SA100: the main Self Assessment tax return for individuals.
- NIC (National Insurance contributions): payments that build entitlement to state benefits.
- MTD (Making Tax Digital): HMRC's digital record-keeping and reporting system.
- P60: the year-end summary of pay and tax from your employer.
Should I use software myself or get an accountant?
Software suits simple affairs: one salary, a small dividend, no other income. An accountant adds value when you have a company, dividends, a vehicle, pensions or rental income, because choices in one place change tax in another. The decision comes down to risk and time, not only the fee.
If you want to compare structures first, read our guide on sole trader versus limited company for Uber drivers. You can also check a rough tax figure with our tax calculator, though a calculator is not a substitute for filing.
How Uber Driver Accountant helps
We work only with drivers, and we are independent of Uber and Bolt. Our fixed fees start from £20 a month, so you know the cost before you begin. We can run your payroll through our payroll service, set up and manage your limited company accounts, and prepare your personal tax return. See our pricing for details.
That means one team looks at payroll, dividends and the return together, so the figures agree. You do not have to choose between tools or reconcile them yourself.
Conclusion and next steps
Payroll software and self assessment software do different jobs, and a limited company director usually needs both. Keep payroll reporting on time through the year, then reconcile the figures before you file your return by 31 January 2027 for 2025/26. When in doubt, ask for help early rather than after a penalty notice.
If you would like us to handle payroll and your return together, contact us for a straightforward conversation.
Last reviewed 3 October 2026 by the Uber Driver Accountant tax team.
This article is general information and is not personal tax advice. Rates, thresholds and deadlines change, so speak to a qualified accountant about your own circumstances. If HMRC raises a dispute or penalty, professional representation is recommended.
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