Limited company guide

Payroll setup for a limited company

Registering as an employer, running RTI payroll and meeting pension duties.

Written and reviewed by Waqas Sagar Member of ICAEW, Fellow of ACCA, Fellow of AAT, a double graduate and entrepreneur at heart, helping startups grow and serving thousands of businesses nationwide with an excellent team. Published by LimitedCompany.Accountants, 12 London Road, Morden, London SM4 5BQ. Reviewed 12 September 2026 against 2026/27 UK rates and current Companies House and HMRC guidance.

What this means for your company

Register for PAYE with HMRC before the first payday, it can take up to a couple of weeks to receive the references. You need a scheme even if the only employee is the director on a salary.

01

Registering as an employer

02

Running payroll

03

Pensions

Registering as an employer

Register for PAYE with HMRC before the first payday, it can take up to a couple of weeks to receive the references. You need a scheme even if the only employee is the director on a salary.

You will receive an employer PAYE reference and Accounts Office reference; both are needed for filing and payment.

Running payroll

A Full Payment Submission must reach HMRC on or before the day employees are paid. An Employer Payment Summary is used to claim the Employment Allowance, report CIS deductions suffered or declare a nil payment.

Pay PAYE and National Insurance by the 22nd of the following month electronically. Employees receive payslips, a P60 by 31 May, and P11Ds for benefits by 6 July.

Pensions

Auto-enrolment duties start from the first employee's start date. Eligible jobholders must be enrolled and given the right to opt out, and a declaration of compliance filed with The Pensions Regulator. A sole director with no employment contract is normally exempt.

Thresholds, rates and deadlines quoted here reflect the 2026/27 UK position. Check current GOV.UK guidance, or ask us, before you rely on them for your own company.

Local help

Talk to a limited company accountant near you

We work with company directors across London and Surrey from our office at 12 London Road, Morden, London SM4 5BQ. Pick your area, or send the form below and we will call you back.

Frequently asked

Payroll setup for a limited company: questions directors ask

Can we pay the director once a year?

Yes. An annual payroll scheme is common for single-director companies, with one FPS a year, but it must be set up as an annual scheme with HMRC.

What if we pay someone as a freelancer?

Employment status depends on the reality of the working arrangement, not the label. Getting it wrong makes the company liable for unpaid PAYE.

What records are needed for payroll setup for a limited company?

Keep bank statements, sales and platform reports, purchase invoices, payroll records, VAT workings, finance agreements and Companies House correspondence. We confirm the exact list at onboarding and identify gaps before a filing deadline becomes urgent.

How much does help with payroll setup for a limited company cost?

The fee depends on transaction volume, record quality, VAT and payroll requirements, historic catch-up and the level of reporting needed. We agree a fixed scope and price before technical work starts, with published packages available on our fees page.

Can you take over payroll setup for a limited company from another accountant?

Yes. We request professional clearance, collect the prior records and authorities, check the next Companies House and HMRC deadlines, and give you one clear handover list. The process is normally completed remotely.

Can payroll setup for a limited company be handled online?

Yes. We work through secure cloud records, scheduled reviews and digital approvals, while keeping a named team available by phone, video call and email. Clients can also visit our Morden office by appointment.

Which accounting software works best for payroll setup for a limited company?

We regularly work with Xero, QuickBooks, FreeAgent, Sage and connected sales or expense apps. The right setup depends on transaction volume, integrations and the reports you need, not simply the software brand.

What tax deadlines matter for payroll setup for a limited company?

The relevant calendar may include annual accounts, Corporation Tax payment and return dates, confirmation statements, VAT returns, payroll submissions and Self Assessment. We map the dates from your company year end and registrations.

Is this payroll setup for a limited company guidance personal tax advice?

No. This page explains general UK rules and common accounting treatment. Your facts, contracts and wider tax position must be reviewed before you rely on a conclusion.

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Check the current rules

Use official information as your reference point.

Deadlines, thresholds and filing rules change. GOV.UK and Companies House publish the current statutory position; advice should then be applied to your company’s circumstances.

Key tax terms explained

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Pick a time that suits you and a qualified accountant will call you about your company, deadlines and fees.

Appointments run monday to friday, 9:00am to 5:30pm. Your confirmation is emailed straight away.

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