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Are Shopify Fees, Refunds & Payouts Making Your Profit Look Smaller?

Accountants for Shopify

Shopify Accountant & Ecommerce Tax Specialist Across the UK

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Accountants for Shopify

Vexo Accounting is a firm of accountants for Shopify sellers, working with online businesses right across the UK. We handle the bookkeeping, VAT, and tax side of running a Shopify store, so you can spend your time on stock, marketing, and customers instead of spreadsheets.

Whether you run a single Shopify store from a spare room or a multichannel brand doing six figures a month, we built our accounting services around how Shopify actually works, not around a generic bookkeeping template that was never designed for online sellers. For UK-based Shopify sellers, the numbers only get harder to manage as the business grows, and that is exactly where we come in.

Shopify is not the only ecommerce platform out there, but it is where most of our clients trade, and it is where we have built the deepest expertise. If you are searching for a Shopify accountant who will actually look at your online store rather than just your bank statements once a year, that is what Vexo Accounting does every day.

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Why Shopify Sellers Across The UK Need An Accountant Who Gets How The Platform Works

Online selling is not a side hustle anymore. In June 2026, 29.4% of all UK retail sales happened online, the highest share since April 2021, and online spending was 11.7% higher than the same period the year before. That is a lot of Shopify stores doing real trade, not hobby projects.

Online spending made up 50.5% of total UK card spending in September 2025, compared with 43.7% back in September 2019. Shopify businesses are not running a niche channel anymore. They are running mainstream UK retail businesses that happen to trade through a website instead of a shopfront.

A general accountant can file your tax return. But Shopify creates its own accounting problems that a standard bookkeeper rarely sees day-to-day.

Payouts arrive net of fees, not the gross amount your customer paid. Refunds, chargebacks, and currency conversion sit between your sales and your bank balance. If your accountant does not understand that, your numbers will be wrong before you have even started.

Shopify accounting is not the same job as general bookkeeping, and treating it that way is where most mistakes start. A specialist Shopify accountant looks at payouts, fees, and channel data in a way that a general ecommerce accountant might miss entirely, because Shopify was never built to fit neatly into standard accounting software.

Not every specialist accountant understands Shopify inside out, which is exactly why we built our service around it rather than adding it as an afterthought. Ecommerce accounting is not simply bookkeeping with extra steps. It needs its own approach, and that is the gap we fill.

That is why so many Shopify businesses come to us after outgrowing a general practice accountant who was never set up for ecommerce in the first place.

Accountants For Shopify
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What Our Shopify Accounting Service Actually Covers For Your Business

What Our Shopify Accounting Service Actually Covers For Your Business

We built our service around the jobs a Shopify business actually needs done well. This is the job description of a proper Shopify accountant, not a bolt-on service tacked onto a standard bookkeeping package. Here is what that looks like in practice.

We Reconcile Your Shopify Payments Payouts Down To The Last Penny

Shopify Payments payouts rarely match your gross sales figure. Transaction fees, refunds, and chargebacks are already deducted by the time the money lands in your bank account.

We reconcile your Shopify payouts every single week against your actual Shopify sales data, so your bookkeeping shows what really happened rather than a rounded guess. Getting this wrong is one of the most common mistakes we see among Shopify businesses.

It makes your gross sales look smaller than they are, and your payment processing fees disappear into thin air. That throws your real Shopify profit off for the whole month.

Any Shopify accountant worth paying should be doing this as standard, not once a quarter when the VAT return is due, so your Shopify payouts always tie back to the sales that created them. Good Shopify accounting starts with accurate reconciliation, not a once-a-year clean-up.

We Connect Shopify To Xero Or QuickBooks So Nothing Gets Entered Twice

Manual data entry is slow, and it invites mistakes. We set up a proper connection between your Shopify store and cloud accounting software, usually Xero or QuickBooks, so sales, fees, and payouts flow through automatically instead of being typed in by hand.

This cuts manual data entry down to almost nothing and saves hours of work every month. The difference between an ecommerce accountant and a Shopify specialist often comes down to exactly this level of detail.

It also gives you accounting processes and financial processes that hold up under scrutiny, whether that is from HMRC, a lender, or an investor looking at your financial statements.

We connect a range of ecommerce bookkeeping tools where they add value, from Link My Books through to simple exports for smaller stores, so payouts get broken into clean, accurate accounting records rather than one messy lump sum. A Shopify accountant who is still doing this by hand in a spreadsheet is not saving you money. They are costing you accuracy.

We Handle VAT On Shopify Sales, Including Sales Into The EU

There were around 2.29 million VAT-registered traders in the UK in 2024/25, with 234,000 new VAT registrations that year. Once your taxable turnover crosses the VAT threshold, currently £90,000, you need to register for VAT and start filing returns on a set schedule, whether you feel ready or not.

We handle VAT registration, check that your Shopify tax settings actually match your VAT compliance obligations, and file your returns on time. Shopify changed its own UK tax setup in May 2026, retiring Basic Tax for new UK stores in favour of Shopify Tax or manual tax settings. Because this change came directly from the Shopify platform itself, sellers who do not update their settings can end up charging the wrong amount of VAT without realising it.

The wholesale and retail sector accounts for around a third of the UK's net VAT bill, roughly £57 billion in 2024/25, so HMRC pays close attention to this sector. Getting VAT compliance wrong is one of the most expensive mistakes a growing Shopify business can make, and your VAT obligations do not disappear just because you did not know about them.

If you have not needed to register for VAT yet, we will flag it well before the threshold catches you out, not after. Your Shopify accountant should be checking this every quarter, not just once a year.

We Manage Multiple Currencies And International Sales

If you sell to customers outside the UK, you are dealing with multiple currencies, exchange rate movements, and international customers who can trigger extra tax rules once you pass certain thresholds abroad. EU Shopify sales in particular can create their own VAT registration requirements once volumes build up in individual countries.

Selling outside the UK does not stop at VAT either. Customers in the United States can trigger sales tax obligations in individual states once your sales there cross certain thresholds, and sales tax rules vary from state to state in a way that catches a lot of Shopify sellers out. We help clients understand when US sales tax becomes relevant and when it can safely be left for another day, since not every Shopify accountant is confident advising on sales tax outside the UK.

We keep your financial records accurate across every currency you trade in, so your reports reflect real sales revenue rather than a number distorted by exchange rate swings on the day we happen to run your books.

We Track Inventory, Cost Of Goods Sold, and Product-Level Profit

Inventory management is where a lot of ecommerce businesses lose track of their real numbers. Stock sitting in a warehouse ties up cash, and if your cost of goods sold is not tracked properly, your profit figures are basically guesswork dressed up as accounting.

We handle inventory valuation properly, track inventory against sales as it moves, and can show you profit at the product level rather than one combined number for the whole Shopify store. Getting inventory valuation right also protects your corporation tax position, since overstated stock values can inflate your taxable profit without you realising it. Poor inventory management is one of the quickest ways to lose sight of real profit in a growing Shopify business, and a good Shopify accountant tracks this properly rather than estimating it once a year.

We Show You Real Profit After Advertising Costs, Fees, and Returns

Turnover on its own tells you very little. A product can have strong sales revenue and still lose money once you account for advertising, payment processing fees, shipping, and returns.

We help you work out contribution margin properly, so you know what is genuinely left over from each sale once product cost, fulfilment, advertising, and Shopify Payments fees are stripped out. That includes checking whether promotions, discount codes and free shipping offers are actually profitable once every cost is counted, rather than assuming a busy sales period automatically means a good one. This is where a specialist Shopify accountant earns their fee, because turnover on its own tells you very little about what you actually kept.

We Build Cash Flow Forecasts So You Are Never Caught Short On Stock

Cash flow forecasting matters more in ecommerce than almost any other type of business, because you often pay for stock weeks or months before you sell it. Cash flow is one of the biggest reasons ecommerce businesses run into trouble, even ones that look profitable on paper. Many ecommerce businesses fail not because they are unprofitable, but because they run out of cash at exactly the wrong moment.

We help you manage cash flow with forecasts built from your actual Shopify sales data, not guesswork, so you know when your next stock order needs paying for and whether the business can afford it. Ask any Shopify accountant who has worked with a fast-growing store about cash flow, and they will tell you the same thing. Good cash flow management is often the difference between a Shopify business that scales smoothly and one that stalls at exactly the point it should be growing fastest.

We Bring Multichannel Sales Into One Accurate Set Of Numbers

Plenty of Shopify sellers do not sell through Shopify alone. Research covering 2025 found that 24% of UK adults mainly buy physical goods online, while 29% split their shopping evenly between physical shops and online channels. That mix often shows up as one business selling through a Shopify store, a physical shop, and one or two marketplaces at the same time.

Many ecommerce businesses only realise how disconnected their channels are once they try to work out real profit across all of them. If that sounds like your business, we bring every channel into one set of financial reports, so you get one accurate picture of your business finances instead of three or four systems that do not talk to each other.

Keep Your Shopify Store Finances Clear and Organised

Let Vexo Accounting manage your Shopify sales, payment fees, bookkeeping, VAT and tax, with specialist accounting support for your online store.

How Much Does Shopify Accounting Cost in the UK?

We looked at UK ecommerce accounting fees from a range of firms during 2026 to build a fair average, rather than pulling a number out of the air.

Across the sources we checked, monthly accounting services for smaller, single-channel Shopify stores generally start around £50 to £100 a month. VAT-registered Shopify businesses with more order volume, multiple channels, or international sales tend to sit between £150 and £300 a month, and larger, high-volume sellers can pay £300 to £500 or more once payroll, management accounts, and multi-currency work are added in.

Our own pricing for most Shopify sellers tends to fall in the £90 to £280 a month range, based on recent projects, depending on order volume, VAT status, and how much cleanup work is needed at the start. Cheaper packages sometimes exclude the accounting software costs entirely, so always check what is included before comparing prices. Any Shopify accountant should be able to ask about your channel mix, order volume, and VAT status before quoting a number that actually means anything.

This is a rough guide and the actual cost varies depending on your circumstances. We give every client a fixed quote before any work begins, so you always know exactly what you are paying and why.

How Much Does Shopify Accounting Cost in the UK
WHY CHOOSE VEXO ACCOUNTING

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Why Shopify Sellers Choose Vexo Accounting As Their Specialist Shopify Accountant

Why Shopify Sellers Choose Vexo Accounting As Their Specialist Shopify Accountant

We are chartered accountants, not a general bookkeeping service that added the word ecommerce to a website. Our team has built genuine ecommerce expertise around Shopify, Shopify Payments and the accounting software that connects to them.

A specialist Shopify accountant should understand your business finances well enough to spot a problem before it turns into a letter from HMRC. We keep your accounting processes tight, your financial reports accurate, and your tax compliance up to date, including corporation tax, income tax and self assessment for company directors. We also make sure you always know what you need to pay income tax on each year, well before your filing deadline arrives.

That commitment to accurate financial reporting is what keeps clients with us for years, not just one tax season. Our ecommerce clients range from single-founder Shopify stores to multi-brand groups turning over seven figures, and that is what being a specialist Shopify accountant actually means at Vexo Accounting, rather than being a general ecommerce accountant who occasionally works with online sellers.

We keep your business finances separate from your personal finances from day one, which sounds obvious but catches out a surprising number of growing Shopify businesses. As chartered accountants, we can also handle the entire accounting process end to end, from your first Shopify sale through to your annual accounts and self assessment.

Every client gets a dedicated point of contact rather than a rotating cast of junior staff, and we explain what your numbers actually mean in plain English, not jargon. That level of tax compliance is not optional once you are VAT registered and growing fast, and it is the standard we hold our Shopify accounting to every single month.

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Here Is How Working With Vexo Accounting Works From Enquiry To Ongoing Support

Getting started is simple. We start with a short call to understand your Shopify store, your current bookkeeping software, and where things are currently going wrong.

From there, we connect your accounts, clean up your financial data where needed, and set up accurate bookkeeping practices going forward using cloud accounting tools that fit your business. Most clients are fully onboarded within a couple of weeks, with clear financial reports landing in your inbox after that, so you always know where you stand without having to ask. We reconcile every one of your financial transactions properly from month one, not just the ones that are easy to explain, so you always have a clear read on the financial health of your Shopify business.

We stay on top of Making Tax Digital requirements as they roll out across income tax, VAT, and beyond, so you are never scrambling to meet a new HMRC deadline you did not know was coming. If HMRC ever has a question about your Shopify business, we deal with it directly on your behalf. Your Shopify accountant should be easy to reach, not hidden behind a ticket system, and that is exactly how we work as a responsive accountancy firm.

Here Is How Working With Vexo Accounting Works From Enquiry To Ongoing Support

Need Help With Your Accounts or Tax?

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Get A Free Quote From Vexo Accounting Today

Get A Free Quote From Vexo Accounting Today

If you want a Shopify accountant who actually understands payouts, VAT, and inventory, get in touch with Vexo Accounting for a free quote. Tell us about your Shopify store, your sales channels, and where your bookkeeping currently stands, and we will come back with a fixed price and a clear plan.

You built a Shopify business worth looking after properly. Vexo Accounting is ready to be the Shopify accountant your business has been missing, whether you are just past the VAT threshold or already running seven figures through Shopify Payments. Request your free quote from Vexo Accounting today and find out exactly what specialist Shopify accounting would cost for your business.

FAQS

Frequently Asked Questions

Clear answers to the most common questions about our accounting services.

What does a Shopify accountant do?

A Shopify accountant manages the bookkeeping, VAT, tax and financial reporting needs of an online store, including Shopify Payments payouts, fees, refunds, chargebacks and inventory. A specialist Shopify accountant also connects Shopify with software such as Xero or QuickBooks to keep the accounts accurate.

Why do Shopify businesses need specialist accountants?

Shopify businesses need specialist accountants because payouts do not normally match gross sales once fees, refunds and chargebacks have been deducted. A Shopify accountant understands these platform-specific transactions and can reconcile them properly rather than treating the store like a standard business.

How much does a Shopify accountant cost in the UK?

A Shopify accountant in the UK typically charges according to order volume, VAT status, sales channels and the amount of bookkeeping or clean-up required. Smaller stores may start around £50–£100 per month, while Vexo Accounting’s Shopify clients generally pay £90–£280 per month depending on their requirements.

Can a Shopify accountant handle Shopify Payments reconciliation?

A Shopify accountant can reconcile Shopify Payments payouts against your underlying sales, fees, refunds and chargebacks. Regular reconciliation ensures the figures recorded in your accounts reflect the actual Shopify transactions rather than only the net amount received in your bank account.

Can a Shopify accountant handle VAT for my Shopify store?

A Shopify accountant can handle VAT registration, check your Shopify tax settings and prepare and file your VAT returns. For UK businesses, VAT registration is generally required once taxable turnover exceeds the current £90,000 threshold, with international sales potentially creating additional VAT obligations.

Can a Shopify accountant connect Shopify to Xero?

A Shopify accountant can connect Shopify to Xero so sales, fees and payouts can flow into your accounting records without repeated manual data entry. Vexo Accounting also works with QuickBooks and ecommerce bookkeeping tools such as Link My Books where they suit the store’s requirements.
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