Pay and RTI
We calculate pay, tax, National Insurance and deductions, then send a Full Payment Submission to HMRC on or before payday.
Payslips for every employee- Employer Payment Summary when needed
Payroll services
Payroll for Small eCommerce Businesses
PAYE, RTI submissions, pensions and director pay, handled by the same team that does your accounts. Payroll for small business that runs alongside your bookkeeping, not separately from it.
Book a discovery call 
- RTI submissions to HMRC every pay run
- Auto-enrolment pensions managed
- Director salary and dividends planned together
In short
eCounts runs outsourced payroll for UK eCommerce businesses, from a single-director company paying a salary to a growing team with seasonal staff. We process pay, send Real Time Information (RTI) reports to HMRC, manage auto-enrolment pensions and year-end forms, and plan director salary alongside dividends and corporation tax because we also keep your books.
Works with the platforms and software you already use
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Amazon -
Shopify -
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Etsy -
TikTok Shop -
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Xero -
QuickBooks - A2X
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PayPal -
Stripe -
Klarna
Trademarks belong to their owners. eCounts is independent and not endorsed by these platforms.
Director salary
Director salary and dividends: the considerations for 2026/27
Most owner-managed eCommerce companies pay their directors through a mix of a modest salary and dividends. There is no single right answer. The best mix depends on your other income, whether the company has other employees, its profits and your plans, so we review it each year rather than applying a formula. Payroll sits alongside the other eCommerce accounting services we provide, which is what makes that review possible.
The figures that shape the decision for the 2026/27 tax year are:
- Personal allowance of £12,570. Salary up to this level is free of income tax if you have no other income.
- Employee National Insurance starts at the primary threshold of £12,570, at 8% up to £50,270 and 2% above.
- Employer National Insurance is 15% on pay above the secondary threshold of £5,000.
- Lower earnings limit of £6,708. Salary at or above this level normally counts towards your State Pension record.
- Employment Allowance of up to £10,500 can reduce employer National Insurance, but not if a sole director is the only employee paid above the secondary threshold.
- Dividends come out of profits after corporation tax. The first £500 is covered by the dividend allowance, then dividends are taxed at 10.75%, 35.75% or 39.35% depending on your tax band.
Salary and employer National Insurance are usually deductible for corporation tax, while dividends are not, which is why the decision belongs with whoever prepares your management accounts and corporation tax.
What is included
What our payroll services cover
Everything an employer has to do on payroll, run on a fixed monthly rhythm.
Pensions
We assess staff for auto-enrolment, enrol eligible workers, calculate contributions and handle re-enrolment every three years.
- Opt-ins and opt-outs managed
- Re-declaration of compliance
Year end
We send the final submission of the tax year and produce P60s, which employees must have by 31 May.
- P11D reporting by 6 July
- Leavers' P45s
In your accounts
Payroll journals post into Xero or QuickBooks, so wages, National Insurance and pension costs land in your books correctly.
- No re-keying
- Liabilities reconciled monthly
The monthly rhythm
Key payroll deadlines for employers
These are the HMRC deadlines we work to on your behalf.
| Task | Deadline |
|---|---|
| Full Payment Submission (FPS) | On or before each payday |
| Employer Payment Summary (EPS), when needed | By the 19th of the following tax month |
| Pay PAYE and National Insurance to HMRC | By the 22nd of the following tax month if paying electronically |
| P60s to employees | By 31 May after the tax year ends |
| P11D and P11D(b) for expenses and benefits | By 6 July after the tax year ends |
Tax months run from the 6th of one month to the 5th of the next. Source: GOV.UK.
Employing people in eCommerce
Payroll for online sellers is rarely simple
eCommerce payroll has its own patterns. Q4 often brings temporary packing and warehouse staff, many roles are part-time or variable hours, and holiday pay for irregular hours needs calculating properly. Temporary staff still need to go through payroll, and from 1 April 2026 everyone aged 21 and over must be paid at least the National Living Wage of £12.71 an hour.
Family members on the payroll are common, and perfectly legitimate when the work is genuine and the pay is reasonable for it. We will help you document it so it stands up if HMRC asks.
Freelancers are the other big area: designers, photographers, agencies and virtual assistants. Where a small company engages a contractor through their own limited company, the off-payroll rules generally leave the employment status decision with the contractor's company, but genuine self-employment still matters. We can talk through where the lines sit for your setup. If you are planning to take on staff for peak, build the cost into your cash flow forecast first.
Why one provider
Outsourced payroll with your accountant, not a separate bureau
Payroll on its own is a process. Payroll alongside your accounts is part of your tax planning.
Separate payroll bureau
- Runs the numbers it is given
- Journals often re-keyed into your accounts
- Director pay set without the tax picture
- Two providers to ask when something looks wrong
Payroll with eCounts
Director salary planned with dividends and corporation tax- Payroll journals land in Xero or QuickBooks directly
- Pension and benefit costs visible in your management accounts
- One UK team that knows the whole picture
Benefits and expenses
P11Ds and the move to payrolling benefits
If you provide benefits such as a company car or private medical cover, they currently have to be reported to HMRC, either on a P11D or by payrolling them. HMRC is making payrolling mandatory in phases: company cars, fuel, vans and medical benefits from 6 April 2027, and most other benefits from 6 April 2028.
We will tell you what applies to your business and set up payroll ahead of each change, so the switch does not land on you in the busiest quarter of your year.
Want to know who you would be working with? Read about the eCounts team, see how our fixed fees work on the pricing page, or book a discovery call to talk through your payroll.
Top tips
Four payroll tips for small eCommerce businesses
- 01
Plan director pay before the tax year starts
Decide the salary and dividend mix in advance, then review it when the year's profit is clearer.
- 02
Report on or before payday
Real Time Information reports go to HMRC on or before each payday. Late reports can lead to penalties.
- 03
Plan for peak season staff
Temporary staff for Q4 still need to go through payroll, and may need to be assessed for auto-enrolment.
- 04
Keep payroll and accounts in step
Payroll costs, pension contributions and PAYE liabilities should match your accounts every month, not just at year end.
Coming up
Payroll changes coming up
Benefits in kind move into payroll from April 2027, and Income Tax thresholds stay frozen until 2031.
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MTD for Income Tax threshold falls to £30,000
Sole traders and landlords with qualifying income over £30,000 in 2025/26 must keep digital records and send quarterly updates. Online sellers should check their gross sales, not profit, against the threshold.
Source: GOV.UK, Find out if and when you need to use MTD for Income Tax
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Benefits in kind must go through payroll
Company cars, car fuel, vans, van fuel and employer-provided medical benefits must be reported in real time through payroll, replacing P11D forms for those benefits. Most remaining benefits follow from April 2028.
Source: GOV.UK, Changes to reporting of benefits in kind from April 2027
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MTD for Income Tax threshold falls to £20,000
The threshold drops again, based on 2026/27 income, bringing many smaller Etsy, eBay and side-business sellers into quarterly digital reporting.
Source: GOV.UK, Find out if and when you need to use MTD for Income Tax
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Personal Allowance stays frozen at £12,570
The Personal Allowance and the £50,270 higher rate threshold are frozen until April 2031, as is the Class 4 National Insurance Lower Profits Limit. As profits grow, more of them are taxed.
Source: GOV.UK, Maintaining Income Tax and NICs thresholds until 5 April 2031
One team for payroll, pensions and your accounts
Talk to us about your directors, staff and seasonal hires. Your payroll is run by a fully UK based team, alongside your books.
Do I need to run payroll as a sole director? 
Usually, yes. GOV.UK says you must register as an employer even if you are only employing yourself as the only director of a limited company. Your salary is then reported to HMRC through RTI each payday, even when no tax or National Insurance is due on it.
How much salary should I pay myself as a director?
It depends on your circumstances, so we review it each year rather than giving a standard figure. The main factors are the £12,570 personal allowance and primary threshold, the £5,000 secondary threshold for employer National Insurance, whether your company can claim Employment Allowance and how much other income you have.
Can I just take everything as dividends?
You can, but it is not always the most efficient approach and dividends can only be paid from available profits. A small salary can use your personal allowance, build State Pension entitlement and reduce corporation tax, so most directors take a mix.
Do I need a pension scheme for one employee?
Yes, if that employee is eligible for automatic enrolment. Generally that means a worker aged at least 22 and under State Pension age earning at least £10,000 a year. A company whose only staff member is a sole director does not have automatic enrolment duties.
Do casual Christmas staff need to go on the payroll?
Yes, temporary and casual employees need to be paid through PAYE like anyone else. They must be paid at least the minimum wage for their age and assessed for pension auto-enrolment.
Can I pay my spouse a salary?
Yes, as long as the work is genuine and the pay is reasonable for the job they actually do. Keep a record of their role and hours, because HMRC can challenge a salary that looks out of line with the work.
Can you take over our payroll part way through the year?
Yes, we can move an existing payroll to us mid-year. We will need year-to-date figures for each employee and details of your PAYE and pension schemes, and we will agree a clean changeover date with you.
