Running an eCommerce business in the UK is rewarding, but it comes with a significant responsibility: meeting your filing obligations to HMRC and Companies House. The process differs greatly depending on whether you operate as a sole trader or a limited company, especially in 2025, where evolving compliance rules, digital tax systems, and tighter VAT monitoring mean that filing late or incorrectly could have costly consequences.

This blog dives into the requirements for both sole traders and limited companies, explaining what needs to be filed, when, and how professional eCommerce accountants can help keep you compliant — and profitable. Whether you’re selling on Amazon, Shopify, eBay, or your own site, this guide will ensure you understand the process and can avoid penalties.

Why Filing Matters for eCommerce Businesses

Many business owners see filing as an administrative chore, but in reality, it’s the backbone of your financial compliance. Filing the right documents with HMRC and (for limited companies) Companies House is not just a legal requirement — it also protects your reputation, builds investor confidence, and keeps you eligible for loans and funding.

For eCommerce businesses, filing also ensures your VAT obligations are correctly reported, sales are properly recorded, and deductions for expenses are accurately claimed.

Section 1: Filing for Sole Traders

A sole trader is the simplest business structure in the UK. You and your business are legally the same entity, meaning all profits are taxed as personal income. While there’s no Companies House registration for sole traders, you still have serious filing obligations with HMRC.

1. Registering with HMRC

If you earn more than £1,000 from self-employment in a tax year, you must register as a sole trader with HMRC. For eCommerce sellers, this means any online sales (minus allowable expenses) count toward this threshold.

eCommerce accountants can help with registration, making sure you select the correct start date for trading and align it with your first Self Assessment period.

2. Filing the Self Assessment Tax Return

As a sole trader, your main filing requirement is the Self Assessment. This includes:

• Declaring all eCommerce sales income

• Deducting allowable expenses (using claiming business expenses rules)

• Reporting VAT if registered

• Paying Income Tax and National Insurance Contributions (NICs)
  
  

If your turnover exceeds the VAT threshold (£90,000 as of 2025), you must register for VAT services and submit quarterly VAT returns.

3. VAT Services for Sole Traders

Even though VAT is often associated with bigger companies, many sole traders in eCommerce are caught out when rapid sales growth pushes them over the VAT threshold. If you fail to register in time, HMRC can apply backdated VAT charges plus penalties.

VAT services offered by specialist accountants ensure:

• Correct VAT scheme choice (Standard, Flat Rate, or OSS/IOSS for EU sales)

• Timely quarterly submissions

• Correct treatment of EU and non-EU exports
  
  

4. Personal Taxation Services

Because sole traders pay tax on profits rather than corporate income, personal taxation services are vital. They help ensure you:

• Claim all allowable deductions (home office costs, software, advertising, etc.)

• Avoid moving into a higher tax bracket unnecessarily

• Use your personal allowance effectively

• File on time to avoid HMRC late payment penalties
  
  

For some sole traders, a p800 form may be issued by HMRC if you’ve overpaid or underpaid tax in previous years. Understanding this form is crucial to reclaiming refunds or settling debts without penalty.

5. The P60 Form for Sole Traders

While the p60 form is usually for employees, sole traders who employ staff in their eCommerce business must issue P60s to employees at the end of the tax year. This ensures your payroll reporting to HMRC is accurate and complete.

6. Penalties for Sole Traders

Failing to file your Self Assessment by the deadline results in:

• £100 instant fine (even if no tax is due)

• Daily fines after three months

• Higher penalties if HMRC believes the error is deliberate
  
  

Using professional eCommerce accountants minimises these risks by handling the entire process for you.

Section 2: Filing for Limited Companies

A limited company is a separate legal entity from its owners. This means it must file both with HMRC and Companies House, and its tax responsibilities differ significantly from sole traders.

1. Registering with Companies House

To operate as a limited company, you must register your business name, director details, and registered office address with Companies House. Once registered, you’ll receive a Company Registration Number (CRN) — essential for all future filings.

2. Corporation Tax Services

Limited companies must pay Corporation Tax on their profits. This requires:

• Filing a Company Tax Return (CT600) with HMRC

• Paying Corporation Tax within 9 months and 1 day after the end of your accounting period

• Using corporation tax services to identify allowable deductions, minimise liabilities, and ensure compliance
  
  

3. Annual Accounts and Confirmation Statement

Every limited company must file:

• Annual Accounts to Companies House (financial performance)

• Confirmation Statement (company details and shareholding structure)
  
  

Failure to file these on time can result in fines and, in extreme cases, your company being struck off.

4. VAT Services for Limited Companies

If your eCommerce turnover exceeds the VAT threshold, you must register for VAT. Many limited companies also voluntarily register for VAT to reclaim input VAT on purchases.

Specialist VAT services for eCommerce ensure compliance with:

• Standard VAT

• Flat Rate Scheme

• OSS/IOSS VAT for EU cross-border sales
  
  

5. Personal Taxation Services for Directors

Even though the company pays Corporation Tax, directors also have personal tax obligations. Personal taxation services help directors:

• Report dividends on their Self Assessment
  
  

• Optimise salary vs. dividend structures
  
  

• Avoid higher-rate tax issues
  
  

• Understand any p800 form notifications from HMRC
  
  

6. The P60 Form for Limited Companies

If your limited company employs staff, you must issue a p60 form to each employee annually. This shows their total pay and deductions for the year. Directors who take a salary will also receive a P60 from their own company.

7. Payroll Services

Running payroll correctly is essential for limited companies. Payroll services ensure:

• PAYE compliance

• Timely Real Time Information (RTI) submissions

• Accurate employee tax and NIC deductions

• Avoidance of HMRC penalties
  
  

8. The Role of eCommerce Accountants

For both sole traders and limited companies, eCommerce accountants offer the advantage of industry-specific knowledge:

• Managing platform fees and multi-currency accounts

• Tracking sales from multiple marketplaces (Amazon, Shopify, eBay, WooCommerce)

• Advising on VAT in cross-border transactions

• Preventing filing errors and missed deadlines
  
  

Key Filing Deadlines to Remember

• Self Assessment Deadline (Sole Traders): 31 January following the end of the tax year

• Corporation Tax Payment (Limited Companies): 9 months and 1 day after accounting period end

• Company Tax Return (Limited Companies): 12 months after accounting period end

• Annual Accounts to Companies House: 9 months after year-end

• Confirmation Statement: Every 12 months
  
  

Missing these deadlines can result in escalating penalties.

Why Professional Help Matters

Filing for eCommerce businesses is not just about ticking boxes — it’s about ensuring your numbers are right, your deductions are maximised, and your compliance is bulletproof. Using VAT services, personal taxation services, and corporation tax services from experienced accountants can make the difference between smooth operations and costly mistakes.

At E2E, our eCommerce accountants specialise in navigating both HMRC and Companies House filing requirements. Whether you’re a sole trader just starting out or a growing limited company, we offer tailored solutions to keep you compliant and profitable.

Avoid the stress. Stay compliant. Grow your business.
Contact E2E today for expert filing support.