Professional e-commerce accountants

Looking for an e-commerce accountant who truly speaks your language? Watch your online business soar with 3E’S Accountants.

As your trusted financial partner, we’ll guide your digital store to new heights with tailored accounting solutions and strategic insights. We specialise in seamless platform integrations and smart automation—saving you hours, eliminating errors, and fueling your expansion.

If you’re ready to boost margins, minimise compliance risks, and unlock greater profitability, you’ve found your solution. Let’s get started!

Understanding e-commerce accounting challenges

Running an e-commerce venture? We get your unique financial challenges. The e-commerce landscape brings complex financial hurdles – from tracking inventory across multiple warehouses to reconciling sales across different platforms that hinder business growth.

At 3E’S, our specialist e-commerce accountants understand these challenges intimately, providing tailored solutions to simplify your finances.

We help you overcome the hurdles of marketplace fees, international transactions, and fluctuating revenue streams, transforming financial obstacles into opportunities for growth.

Specialist e-commerce accountants for online businesses

3E’S provides expert accountants who understand the nuances of online selling. We remove the burden of financial management, allowing you to concentrate on growing your e-commerce venture.

With a strong local presence in Harrow, Birmingham, Stoke-on-Trent, Hitchin, and Milton Keynes, we offer comprehensive e-commerce accounting support backed by our teams’ in-depth industry knowledge.

We are experts in dealing with the varying requirements of all the different sales platforms and the tax laws that apply to each.

Our team of specialist e-commerce accountants is dedicated to providing up-to-date, accurate, and timely financial insights to facilitate informed decision-making and propel your business forward.

Stop letting financial complexities hold you back.

Call us at 020 3772 2555 and discover how we can elevate your business

Or reach us by email at info@3esaccountants.co.uk

Our e-commerce
accounting services

E-commerce account preparation

We prepare UK-compliant financial statements tailored for online sellers, ensuring accurate reporting of sales across Amazon, eBay, Shopify and other marketplaces while meeting HMRC requirements.

Self assessment

Our accountants specialise in filing Self-Assessments for e-commerce traders, maximising allowable expenses like marketplace fees, packaging costs, and home office deductions.

E-commerce bookkeeping

We automate your bookkeeping using HMRC-compliant software like Xero or FreeAgent, tracking VAT, platform fees and business expenses in real-time for MTD compliance.

Financial analysis

Our team provides cash flow forecasts and profit analyses specific to seasonal e-commerce trends, helping you plan for peak periods like Black Friday and January sales.

E-commerce payroll services

We handle PAYE, RTI submissions and auto-enrolment pensions for your UK e-commerce business, ensuring full compliance with HMRC payroll regulations.

Annual accounts

We prepare and file your annual accounts with Companies House and HMRC, meeting all UK statutory requirements for limited companies or sole traders.

Cash flow management

We help UK e-commerce businesses forecast cash positions considering VAT payment dates, seasonal inventory purchases and platform payout cycles.

Setting up e-commerce businesses

We advise on the most tax-efficient UK business structures (limited company vs sole trader) and register you for VAT, PAYE and other HMRC schemes as needed.

Scope of our e-commerce
tax services

Tax planning

We develop UK-specific strategies to minimise tax liabilities for online sellers, including optimal dividend/salary mixes for limited companies.

VAT registration and returns

Our specialists handle UK and EU VAT registration and MTD-compliant quarterly returns and advise on schemes like Flat Rate or Margin schemes for online sellers.

Corporation tax filing

We prepare CT600 returns for UK e-commerce limited companies, ensuring proper treatment of platform fees, inventory costs and R&D tax credits where applicable.

Tax enquiry support

We represent e-commerce businesses during HMRC enquiries, providing detailed records of marketplace transactions and proper expense documentation.

Marketplace tax compliance

We ensure proper UK tax treatment of sales made through Amazon, eBay, Etsy and other platforms, including handling platform fee deductions correctly.

Income tax planning & preparation

We optimise personal tax positions for e-commerce business owners through salary/dividend planning and proper allowance use.

Sales tax compliance

We help online sellers navigate EU VAT obligations (OSS/IOSS schemes) and advise on international tax requirements when selling abroad.

Who we can help

Amazon sellers

We handle FBA accounting complexities, including storage fees, refunds and UK/EU VAT obligations for Amazon marketplace sellers.

WooCommerce stores

We provide seamless financial integration and reporting for WooCommerce stores, ensuring accurate tracking of sales and inventory and simplifying VAT compliance for your online business.

Magento stores

We tailor accounting solutions for Magento’s complex e-commerce platforms, offering robust financial management and reporting to handle its advanced inventory and multi-store capabilities.

ebay stores

We simplify tax compliance for professional eBay UK sellers, correctly categorising business expenses and platform-specific deductions.

Etsy sellers

We help Etsy sellers properly account for handmade goods sales, platform fees and VAT obligations as they grow beyond hobbyist status.

Dropshippers

We implement accounting systems for dropshipping businesses that track supplier costs, shipping fees and profit margins accurately.

Shopify merchants

Our systems integrate directly with Shopify to automate accounting for UK-based stores, including proper VAT treatment of digital and physical goods.

Private brands

We track your true product profitability by reconciling manufacturing costs with marketplace sales and advertising spend.

White label sellers

We streamline accounting for your rebranded products, managing supplier costs and bulk order finances.

Benefits of working with an expert e-commerce accountant

Increased accuracy and efficiency

We automate and streamline your e-commerce financial data, eliminating discrepancies across platforms and ensuring precise inventory and sales tracking

Free up your time

We manage the complexities of marketplace fees, sales tax, and multi-channel reconciliation, allowing you to focus on product development and marketing

Stay tax compliant

We navigate the ever-changing sales tax nexus laws for businesses selling into the US, and VAT regulations specific to online sales, preventing costly penalties and ensuring compliance

Cost-effective

Our tailored e-commerce accounting services optimise your cost of goods sold (COGS) and minimise tax liabilities, maximising your profit margins and reducing unnecessary expenses.

Multi-channel sales reconciliation

We automate the reconciliation of sales from Amazon, Shopify, Etsy, and other marketplaces, providing a unified view of your e-commerce revenue.

No more data headaches!

We consolidate and organise your e-commerce financial data into clear, actionable reports, eliminating the confusion of disparate data sources.

Track sales data and revenue with accuracy

We provide detailed, platform-specific sales reports, enabling accurate analysis of product performance and revenue trends across all your online channels.

Expert advice and support

We offer specialised guidance on inventory management, marketplace fees, and international e-commerce tax implications, helping you navigate the unique challenges of online selling.

Our e-commerce accounting services start from

£200 + VAT
per month

Precision accounting for your e-commerce business.

Call us! Our team is ready to assist weekdays 9 am-5:30 pm.
020 3772 2555

Or reach us by email: info@3esaccountants.co.uk

Future-proofing your
e-commerce
business with 3E’S

E-commerce businesses demand specialised financial management, and 3E’S delivers. Our expert accountants excel in navigating the intricacies of online sales, from diverse payment systems to complex refund processes.

We provide customised solutions that encompass detailed bookkeeping, precise tax planning, and strategic growth guidance. We also ensure your business remains compliant with evolving international tax regulations.

Whether you operate on Shopify, Amazon, Etsy, or multiple platforms, we offer the targeted expertise needed to optimise your financial operations and maximise profitability. We leverage leading software to ensure your financial data is accurate and ready for future investment.

Consider us your strategic partner. We meticulously manage your accounting and tax obligations, allowing you to focus on growing your business, such as expanding your product line, implementing effective marketing campaigns, and driving sales growth.

Connect with our e-commerce accountants now.

How to get started with our e-commerce accountants

At 3E’S Accountants, we make our e-commerce accounting process simple. Here’s how it works:

01

Initial discovery call

We’ll schedule a 30-minute consultation to understand your business model, sales channels, and key pain points – wholly free and obligation-free.

02

Needs assessment

You’ll complete a short digital form detailing your platforms (Amazon/Shopify/eBay), VAT status, and growth goals so we can tailor our services.

03

Proposal and pricing

You’ll receive a transparent, fixed-fee proposal outlining the services best suited for your e-commerce business.

04

Secure client portal setup

We create your encrypted login for our accounting platform (Xero/QuickBooks) with multi-factor authentication for data security.

05

Platform integrations

Our team connects your marketplace accounts (Seller Central, Shopify, etc.) to import sales, fees, and payouts automatically.

06

Document handover

You’ll upload historical records (bank statements, tax filings, inventory reports) via our secure portal – we handle the organisation.

07

VAT & tax compliance check

We audit your past filings (if any) and ensure you align with UK MTD, VAT, and corporation tax rules.

08

Dedicated accountant assigned

You’ll get a single point of contact—an e-commerce accounting specialist familiar with your business.

09

Regular reporting setup

We configure automated financial reports (P&L, cash flow, inventory insights) based on your preferences.

10

Ongoing support

Beyond compliance, we provide proactive tax planning and growth advice tailored to your marketplace sales.

Software used by our e-commerce accountants

We work efficiently across all major platforms, delivering accurate CIS accounting regardless of your system.

Why e-commerce businesses choose 3E’S Accountants?

We don’t just crunch numbers—we build trust, deliver proactive solutions, and speak the language of online sales.

Dedicated client manager

You’ll have an ACCA/ICAEW-qualified specialist managing your accounts who understands e-commerce inside out.

Multi-channel expertise

We seamlessly reconcile your sales across Amazon, Shopify, eBay and other platforms in one consolidated system.

Platform-specific support

Our team knows the unique fee structures and tax rules for every marketplace you sell on.

Save time on account management

We automate 90% of your bookkeeping tasks so you can focus on growing your business.

MTD compliance

Your VAT submissions will always be Making Tax Digital compliant and filed on time.

Regulatory compliance

We keep you protected with up-to-date knowledge of HMRC rules and international tax obligations.

Don't just listen to us - hear what our
clients have to say!

Swapn Patel

Bruton Pharmacy

Industry: Pharmacy

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Unlock your business's growth with our resource hub

Explore our library of industry-leading blogs, financial updates, and actionable trend reports tailored for growth.

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Frequently asked questions

1. Is hiring an accountant necessary for my e-commerce business?

A specialist accountant is crucial for your e-commerce venture’s financial success. Beyond basic number-crunching, we deliver strategic guidance on tax optimisation, cash flow forecasting, and growth budgeting. Our team monitors your critical financial metrics, pinpoints improvement opportunities, and ensures full compliance with evolving UK regulations – transforming your accounting from an obligation into a growth tool.

2. What accounting software works best for e-commerce operations?

For online sellers, we recommend Xero, QuickBooks or FreeAgent – the leading platforms we integrate daily. These cloud-based solutions streamline:

Automated sales reconciliation across marketplaces
Real-time payroll processing
Custom financial reporting
Secure multi-device data access

We’ll help implement the ideal system, matching your sales volume and business complexity.

3. What are the dangers of using a non-specialist accountant?

General practitioners often lack crucial e-commerce expertise, potentially causing:

Missed tax-saving opportunities specific to online sellers
Errors in HMRC reporting that trigger audits
Misunderstood VAT rules (especially for international sales)
Inaccurate treatment of marketplace fees and digital expenses

Our specialist e-commerce accountants eliminate these risks while actively boosting your profitability.

4. How easy is it to switch accountants to 3E'S?

We make transitions seamless through our proven transfer process:

We handle all communications with your current provider
Conduct a comprehensive compliance health check
Reconstruct any problematic historical data
Implement optimised reporting systems
Provide ongoing strategic tax planning

You’ll experience zero downtime while gaining specialised support, letting you refocus fully on business growth.

5. How do you handle VAT for Amazon/Shopify sellers?

We handle VAT for Amazon and Shopify sellers by first assessing their sales across different regions to determine VAT registration obligations. We then manage the registration process, ensure accurate VAT calculations on sales, and handle the submission of regular VAT returns. We also advise on the complexities of distance selling regulations and the Import One-Stop Shop (IOSS) scheme, as applicable.

6. Why do e-commerce businesses need specialist accountants?

Online sellers face unique challenges, such as multi-platform reconciliations, marketplace fees, and international VAT. We automate these processes while ensuring full HMRC compliance, saving you time and maximising deductions.

7. What if HMRC investigates my business?

We provide full audit support – preparing all documentation for marketplace transactions and representing you throughout the enquiry process.

8. What specific accounting challenges do e-commerce businesses typically face?

E-commerce businesses often struggle with inventory management, sales tax compliance across multiple jurisdictions, payment processing complexities, and integrating various online sales platforms with accounting software.

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