Business Managing money

Best Accounting Software for Shopify Sellers in the UK

Saim Jalees

02.07.26

Read time 11 minutes

If you run a Shopify store, bookkeeping can get complicated quickly. You are not just recording sales, you are dealing with payout delays, payment processor fees, refunds, gift cards, VAT, stock movements and sometimes multiple currencies too.

In this guide, we've compared accounting software UK Shopify sellers can consider, with notes on Shopify integrations, VAT support, pricing and where each tool may fit. We've also included source-backed pricing and feature details so you can compare options more clearly.

We've also explained how Wise Business can support international Shopify workflows by helping UK sellers manage cross-border payments, supplier costs and accounting software connections.

Disclaimer: The UK Wise Business pricing structure is changing with effect from 26/11/2025 date. Receiving money, direct debits and getting paid features are not available with the Essential Plan which you can open for free. Pay a one-time set up fee of £50 to unlock Advanced features including account details to receive payments in 22+ currencies or 8+ currencies for non-swift payments. You’ll also get access to our invoice generating tool, payment links, QR codes and the ability to set up direct debits all within one account. Please check our website for the latest pricing information.

⚠️ Note: Accounting software features, pricing, integrations, tax tools, bank feeds, inventory tools and multi-currency support can vary by plan, country, eligibility and provider terms.

Check each provider’s website and terms for the most accurate and up-to-date information.

Summary of software

Software	Summary of features and fees
Xero	Cloud accounting with Shopify and ecommerce app connections, multi-currency tools and VAT return support. Regular pricing currently starts from GBP 16 per month excluding VAT.²
QuickBooks Online	Ecommerce accounting with Shopify Connector by Intuit, stock tracking in higher plans, VAT tools and multi-currency support in relevant plans. Pricing shown in the source starts from GBP 108 per year plus VAT after the promotional period for Sole Trader Plus.^3,4
FreeAgent	Simple accounting for smaller businesses, but its direct Shopify integration was discontinued on 30 April 2025. Limited company pricing is listed at GBP 33 per month excluding VAT.^6,7
Zoho Books	Cost-conscious accounting with a free plan and paid annual-billing plans from GBP 10 per organisation per month. Higher tiers add broader features such as multi-currency and inventory capabilities.⁹
Sage Accounting	Familiar UK accounting software with VAT features and plan-based accounting tools. Current post-promo pricing shown in the source is GBP 20/43/59 per month plus VAT depending on tier.⁵
NetSuite	ERP-level option for larger Shopify operations. NetSuite Connector supports Shopify B2C and B2B, with pricing dependent on platform, modules, users and implementation.⁸

Discover Wise Business 🔍

Xero

Xero is often near the top of the shortlist for Shopify sellers because it is built for cloud accounting and has a strong ecommerce app ecosystem. Its UK ecommerce page says Xero can connect to Shopify, Amazon, eBay or Etsy through ecommerce apps to sync sales and automate accounting.²

The key question is not just whether Xero connects to Shopify, but how cleanly it handles the data once it arrives. For many sellers, the real pain point is that Shopify payouts do not equal sales. Fees, refunds and tax can all sit inside the same payout.

This is where Xero tends to suit growing stores. If you sell in GBP today but expect overseas sales later, the multi-currency angle can matter earlier than you think.

Features

Feature	Details
Ecommerce app connections	Xero says you can connect Shopify, Amazon, eBay or Etsy through ecommerce apps to sync sales and automate ecommerce accounting.²
Shopify connection	Xero says combining Shopify with Xero lets you automatically see Shopify sales and payments in Xero at the end of each day.²
Multi-currency	Xero says its accounting software lets UK ecommerce businesses invoice and accept payments in multiple currencies.²
VAT support	Xero's plan comparison includes submitting VAT returns to HMRC on relevant plans.²
App ecosystem	The source says over 1,000 third-party apps connect with Xero.²

Fees

Fee type	Details
Regular plan pricing	Xero pricing in the source currently starts from GBP 16 per month excluding VAT for Ignite, then GBP 37 for Grow and GBP 50 for Comprehensive.²
Promotions	The source shows promotional pricing for the first 6 months on some plans.²
Shopify seller note	Multi-currency and advanced ecommerce workflows may require checking plan features and connector setup before choosing on headline price alone.

💡 You can connect your Wise Business account to Xero, choose the Wise currencies you want to sync, and feed business transactions into Xero to support your Shopify bookkeeping workflow.

This can help keep international supplier payments, overseas Shopify income and multi-currency transaction records easier to review when reconciling sales, fees and payouts.

QuickBooks Online

QuickBooks Online is a strong fit if you want ecommerce accounting software that feels familiar and is easy to hand over to an accountant or bookkeeper. QuickBooks' UK ecommerce page highlights QuickBooks Plus as an ecommerce accounting solution for taking payments, stock and VAT workflows.³

For many smaller Shopify stores, the appeal is simplicity. If you are not sure whether you need something more advanced, QuickBooks can give you structure for day-to-day bookkeeping, sales tracking and tax preparation without the steeper learning curve of an ERP.

Features

Feature	Details
Shopify Connector by Intuit	QuickBooks says Shopify Connector by Intuit helps automatically share data between Shopify and QuickBooks.³
Stock tracking	QuickBooks says it can track products and costs, with notifications when stock levels are low.³
Sales channel visibility	QuickBooks says Online Plus can show which sales channels are making money.³
VAT support	QuickBooks says users can track VAT, prepare returns and submit to HMRC in line with Making Tax Digital.^3,4
Plan features	The pricing page lists multiple currencies under Essentials and inventory under Plus.⁴

Fees

Fee type	Details
Entry pricing shown	The pricing source shows Sole Trader Plus at GBP 108 per year plus VAT after the promotional period.⁴
Other annual prices shown	The source lists Simple Start at GBP 172 per year plus VAT, Essentials at GBP 410.40 per year plus VAT, Plus at GBP 604.80 per year plus VAT and Advanced at GBP 1,328.40 per year plus VAT after the promotional period.⁴
Payroll	QuickBooks says payroll can be added to Simple Start, Essentials, Plus or Advanced at extra cost.⁴

💡 You can connect your Wise Business account to QuickBooks to support transaction syncing between Wise and your accounting records.

This can be useful for Shopify sellers who receive payments, pay suppliers or manage operating costs in different currencies, then want those transactions reflected in QuickBooks for cleaner reconciliation.

FreeAgent

FreeAgent can suit sole traders, freelancers and smaller limited companies that want simpler bookkeeping and cash flow visibility. But for Shopify sellers, there is an important caveat: FreeAgent says its direct Shopify integration was discontinued on 30 April 2025.⁶

That does not rule FreeAgent out, but it changes who it is best for. If your store has modest volume and you mainly want clean business accounts, basic tax visibility and a lighter system, FreeAgent can still work.

Features

Feature	Details
Shopify workflow	FreeAgent says Shopify transactions now need to be recorded through PayPal workflows or manual accounting, depending on how customers pay.⁶
PayPal route	FreeAgent says businesses using PayPal can connect FreeAgent to PayPal to help populate the account with transactions.⁶
Manual route	FreeAgent says businesses not using PayPal will likely need to account for sales and fees manually by splitting bank transactions.⁶
Smaller business fit	FreeAgent's pricing page positions plans for sole traders, partnerships and limited companies.⁷

Fees

Fee type	Details
Limited company plan	FreeAgent lists the limited company plan at GBP 33 per month or GBP 330 per year excluding VAT.⁷
Eligible bank account access	FreeAgent says access may be included for eligible NatWest, Royal Bank of Scotland, Ulster Bank or Mettle account customers, subject to conditions.⁷
Shopify seller note	The discontinued direct Shopify integration may increase manual work for stores with higher order volumes, refunds or multiple payment routes.⁶

💡 You can connect your Wise Business account to FreeAgent, choose the Wise currencies you want to sync, and feed Wise currency transactions into FreeAgent as new entries.

The connection uses Open Banking and requires your consent to securely share transaction data. Once connected, future transactions can sync automatically to help reduce extra admin when tracking supplier payments, international costs and multi-currency activity.

Zoho Books

Zoho Books is often one of the first alternatives sellers compare when they want cost-conscious ecommerce accounting software. It tends to appeal to merchants who want more built-in capability than entry-level bookkeeping tools without moving straight to an enterprise platform.

Its biggest strength is value for money. But the main thing to test is workflow fit: Shopify integration, VAT handling, stock setup and reporting need to match the level of detail your team actually needs.

Features

Feature	Details
Free and paid plans	Zoho Books lists a free plan plus Standard, Professional and Premium plans in the extracted pricing comparison.⁹
Multi-currency	Zoho's pricing comparison lists multi-currency invoicing and multi-currency transactions in relevant plan areas.⁹
Banking	Zoho's pricing comparison lists bank reconciliation and transaction rules in the banking section.⁹
VAT	Zoho's pricing comparison includes VAT tracking, VAT returns and MTD VAT filing in its feature list.⁹
Inventory	Zoho's pricing comparison includes advanced inventory in its feature list.⁹

Fees

Fee type	Details
Annual-billing monthly equivalents	Zoho Books pricing shown in the source includes GBP 0, GBP 10, GBP 20 and GBP 25 per organisation per month when billed annually for the visible Free, Standard, Professional and Premium tiers.⁹
Plan limits	The source lists plan differences including users, invoice volumes and expense/bill limits.⁹
Shopify seller note	Lower monthly pricing should be weighed against whether Zoho's ecommerce workflow gives your store enough automation and reporting detail.

💡 You can connect your Wise Business account to Zoho Books to support transaction syncing with your bookkeeping workflow.

This may help Shopify sellers keep international supplier payments, overseas sales income and multi-currency activity easier to track alongside invoices, expenses, VAT records and reports in Zoho Books.

Sage Accounting

Sage Accounting makes sense for UK sellers who want a familiar accounting brand and a straightforward route into ecommerce bookkeeping. It is especially relevant if your team already knows Sage, or if you want software that feels closer to traditional SME finance processes.

The main advantage here is familiarity. When you are trying to sort Shopify VAT accounting, payout timing and stock reporting, a familiar system can shorten setup time and reduce errors.

Features

Feature	Details
VAT focus	Sage's accounting page describes MTD for VAT returns and VAT features across its accounting plans.⁵
Plan range	Sage lists Start, Standard and Plus plans for different business needs.⁵
Inventory	Sage says Accounting Plus includes Standard features plus financial budgets, inventory management and multi-currency support.⁵
Flexibility	Sage says users can upgrade, change or cancel plans at any time.⁵

Fees

Fee type	Details
Current post-promo pricing	Sage states that after the promotional period, pricing is GBP 20/43/59 + VAT per month depending on tier.⁵
VAT treatment	Sage states that all pricing excludes VAT.⁵
Trial or promotion	The source mentions a promotional offer and an option to skip the offer for a free trial period.⁵

NetSuite

NetSuite is the option on this list for businesses that have moved beyond basic bookkeeping and into operational complexity. NetSuite Connector supports Shopify B2C and B2B, plus other ecommerce and marketplace channels.⁸

That matters because once you scale internationally, accounting stops being a standalone task. Inventory, fulfilment, purchasing and finance all start affecting each other.

Features

Feature	Details
Shopify support	NetSuite Connector lists Shopify B2C and B2B among supported ecommerce applications.⁸
Order and inventory flows	NetSuite says Connector can manage product details, pricing and inventory levels in NetSuite while receiving orders and customer information from ecommerce applications.⁸
Fulfilment updates	NetSuite says order status updates can be updated automatically in the ecommerce system as orders are fulfilled and shipped.⁸
Financial processing	NetSuite says settlement reports, refunds, returns and cancellations are processed automatically with certain ecommerce applications.⁸

Fees

Fee type	Details
Pricing model	NetSuite says pricing is made up of three main components: core platform, optional modules and number of users.⁸
Implementation	NetSuite says there is also a one-time implementation fee for setup.⁸
Connector module	NetSuite Connector is available as an add-on module.⁸

How to choose Shopify accounting software

Choosing the best accounting software for a Shopify store is not just about picking the lowest price. It is about whether the software can explain how gross sales become net cash.

Start by checking your order volume, payment methods, refund pattern and VAT position. Then test how each tool or connector maps sales, taxes, fees and clearing accounts before you rely on it for month-end.

That matters even more once your UK business is VAT-registered. HMRC says you must register for VAT if your total taxable turnover for the last 12 months goes over GBP 90,000, or if you expect it to go over GBP 90,000 in the next 30 days.¹

This publication is provided for general information purposes and does not constitute legal, tax or other professional advice from Wise Payments Limited, its subsidiaries or affiliates. It should not be treated as advice from, or a communication with, HMRC, and it is not intended as a substitute for obtaining business advice from a tax advisor or any other professional.

For smaller stores, Xero, QuickBooks, Sage, FreeAgent or Zoho Books may be enough if the workflow is set up carefully. For larger stores with multiple entities, warehouses or international operations, NetSuite may be worth reviewing.

💡 With Wise Business, you can connect and sync every business transaction to your favourite accounting software, including Xero, Quickbooks, and more.

Manage international Shopify payments with Wise Business

For UK Shopify sellers comparing accounting tools, international payouts, supplier payments and currency conversion can all affect reconciliation.

Wise Business can help you manage international business payments and connect transactions with accounting software, so your bookkeeping workflow has clearer payment data to work from.

With Wise Business, you can:

🌍 Send money to 70+ countries at the mid-market exchange rate with low, transparent fees and no hidden exchange rate markups (product availability varies by region)
📥 Receive payments in 24 currencies and counting
💵 Get local account details for 8+ currencies, including USD and EUR, to let your customers pay in a currency they know and trust - convenience for them and peace of mind for you
💰 Hold money in 40+ currencies
🔁 Convert currencies anytime at the mid-market exchange rate with low, transparent fees
⚡ Use the batch payments tool to create and send up to 1,000 payments in a single transfer
👥 Run payroll and make international payments for up to 1,000 employees all over the world - including paying suppliers using local payment methods like ACH, SEPA, and Faster Payments
💳 Get business debit cards with 0.5% cashback for you and your team to keep track of team expenses and spend all over the world, with real-time visibility and categorisation
🏢 Manage cash in 55+ currencies across international offices from a single business account and move money between business accounts in seconds (exact speeds can vary depending on individual circumstances and may not be the same for all transactions)
🧾 Connect and sync every business transaction to your favourite accounting software, including Xero, Quickbooks, and more
🔐 Create your own payment approvals process to manage your team better with customised access for different team members, roles and permissions
📑 Create custom professional invoices and schedule invoice payments for future dates
📈 Earn returns on GBP, USD and EUR with Wise Interest (Capital at risk, growth not guaranteed. Your money is at risk if governments default or interest rates go negative. Visit https://payout-surge.live/gb/interest/%3C/a%3E to find out more)

🔗 Create payment links and QR codes to get paid easily (Card payment acceptance for new Wise Business customers is currently unavailable. Payment methods subject to eligibility and availability.)
⚙️ Automate payouts with the Wise API (comes with 24/7 customer support, a sandbox account to test integrations, API tokens, and clear documents on how to implement and make the most of our API)

Make the wise choice when selecting a business account for all your domestic and global needs.

Be Smart, Get Wise.

FAQs

What is the best accounting software for Shopify in the UK?

There is no single best option for every seller. Xero and QuickBooks Online are often strong all-round picks for UK Shopify businesses, while Sage can suit teams that want a familiar UK setup.

FreeAgent can work for simpler businesses, Zoho Books may suit cost-conscious sellers, and NetSuite is usually better for larger operations.

Do I need accounting software if I already use Shopify reports?

Usually, yes. Shopify reports show sales activity, but they are not a full accounting system.

Proper bookkeeping still needs bank reconciliation, expense coding, VAT treatment and a clear record of how gross sales became the net payout that reached your account.

How do you reconcile Shopify payouts?

You reconcile payouts by breaking each one into its parts: sales, VAT, fees, refunds, chargebacks and the final deposit.

If you only book the net payout, your revenue and tax reporting can be wrong even when the bank balance looks right.

Does Shopify integrate with Xero or QuickBooks?

Yes. Xero says Shopify sales and payments can appear in Xero at the end of each day through its Shopify connection, while QuickBooks highlights Shopify Connector by Intuit.^2,3

The method still matters, because higher order volumes, refunds and multiple payment methods may need a cleaner connector setup.

What accounting software is best for Shopify VAT?

The best option is the one that helps you keep clean VAT records and prepare reports that are easy to review before filing.

For many UK sellers, that can mean Xero or QuickBooks, while Sage can also work well if you prefer its setup and add the right ecommerce workflow.

Sources:

Sources last checked on 2 July 2026

*Please see terms of use and product availability for your region or visit Wise fees and pricing for the most up to date pricing and fee information.

This publication is provided for general information purposes and does not constitute legal, tax or other professional advice from Wise Payments Limited or its subsidiaries and its affiliates, and it is not intended as a substitute for obtaining advice from a financial advisor or any other professional.

We make no representations, warranties or guarantees, whether expressed or implied, that the content in the publication is accurate, complete or up to date.