HMRC and Companies House Compliance: What UK eCommerce and Medical Businesses Must File

Running a business in the UK means dealing with more than just day-to-day operations. Whether you're dispatching orders from an online shop or managing patient records in a private clinic, staying compliant with HMRC and Companies House is non-negotiable.

While both the eCommerce and medical sectors are growing rapidly, they come with unique financial structures—and different paperwork to match. From tax returns to VAT submissions, understanding what you need to file (and when) is critical. In this blog, we cover the key forms required by HMRC and Companies House and explain how having a specialist in digital retail finance or a healthcare financial advisor by your side can make all the difference.

1. Annual Company Accounts – For All Limited Companies

If your business operates as a limited company, you are legally required to submit annual accounts to Companies House. These include a balance sheet, a profit and loss account, and a director’s report.

For eCommerce sellers, especially those using platforms like Amazon, Shopify, or WooCommerce, reconciling multiple revenue streams, foreign currencies, and merchant fees can complicate this process. A qualified online retail bookkeeper ensures your reports reflect accurate, consolidated data.

Similarly, private practices or healthcare organisations must also navigate equipment purchases, insurance payments, and payroll complexities. Having a dedicated financial advisor for medical professionals helps keep those figures in order and fully compliant.

2. Company Tax Return (CT600) – Sent to HMRC

All limited companies must submit a Company Tax Return (CT600) each year. This form outlines your business's income, expenses, and the tax owed on your profits.

In eCommerce, understanding fulfilment costs, advertising spend, and platform commissions is key. Without clear categorisation, you risk overpaying or under-declaring. A certified eCommerce accounting expert in London is familiar with these specific cost structures and can ensure you claim every legitimate deduction.

In the medical industry, expenses like medical supplies, licensing fees, or staff training must be accurately reported. A seasoned clinic tax specialist knows which costs qualify and how to avoid the red flags that trigger audits.

3. VAT Returns – Quarterly (If Registered)

VAT is where many businesses trip up—especially online retailers and private practices offering both taxable and exempt services. If your taxable turnover exceeds the VAT threshold (currently £90,000), you must register for VAT and file quarterly returns.

eCommerce sellers with cross-border sales, discounts, and returns face particularly tangled VAT scenarios. The UK digital eCommerce VAT specialist can guide you through flat rate schemes, thresholds in other countries, and post-Brexit changes.

Medical professionals may assume their services are VAT-exempt, but it’s not always so straightforward. Cosmetic procedures, for instance, may require VAT registration depending on how they’re classified. A trusted healthcare VAT advisor ensures you’re applying the correct rates without risking compliance errors.

4. Self Assessment – For Sole Traders and Directors

If you’re a sole trader or a company director earning dividends or other personal income, you must file a Self Assessment Tax Return. eCommerce sellers just starting out or medical professionals running a side consultancy often fall under this requirement.

Filing this correctly involves knowing which personal and business expenses to claim. A freelance seller’s tax consultant or doctor’s personal finance expert can help structure your records for HMRC approval, minimising your tax liability without overstepping boundaries.

5. Payroll and Pensions – If You Employ Staff

If your business employs staff—whether warehouse workers, admin staff, nurses, or receptionists—you must run a PAYE payroll scheme and submit returns to HMRC each month. Additionally, eligible employees must be enrolled in a workplace pension, with contributions reported to The Pensions Regulator.

Payroll isn’t just about numbers—it’s about responsibility. Miscalculating even a single paycheque or missing a pension filing can lead to investigations. Having a digital business payroll specialist or a clinical finance manager ensures payroll is handled smoothly and compliantly.

Staying Compliant Without Losing Focus

In both eCommerce and medical fields, it’s easy to feel overwhelmed by the forms and filings required to remain compliant. But compliance isn’t just ticking boxes—it’s a reflection of your business’s professionalism and integrity.

That’s why many forward-thinking businesses in these sectors choose to partner with financial specialists who understand the nuances of their industries. Whether you need help with tax returns, bookkeeping, VAT, or long-term planning, E2E Accounting offers tailored support that fits around your schedule and sector.

Contact E2E today for expert, practical support that keeps you HMRC and Companies House compliant, without the headaches. Want to learn how we help businesses like yours thrive? Discover More about E2E and how we support both digital and healthcare clients with precision-led, industry-focused accounting.