The Best Accounting Software for Shopify Users

The best accounting software for Shopify allows business owners to simplify the tasks of managing cash flow and finances for their online stores.

Today’s entrepreneurs are often reliant on a huge selection of different apps and tools in their day-to-day lives, from collaboration services to website builders and payment systems.

The more you can bring your various tools together into the same environment, the more efficient your workflows become. Fortunately, Shopify can help with this. One of the reasons why Shopify stands as one of the most popular ecommerce and website-building tools in the market today, is it allows you to integrate multiple different apps and tools into your store.

You can link your accounting and bookkeeping software to your website, and keep your reports directly updated from Shopify. The question is:

Which are the best accounting apps for Shopify users?


Freshbooks is one of the better-known accounting software solutions on the market today. It’s both MTD compliant and HMRC approved. Plus, it’s packed with features to make life easier for business leaders. You can use Freshbooks to automatically track unlimited expenses, send estimates, and set up recurring billing or client retainers.

Users can invite their accountant to access Freshbooks alongside them, and discover the benefits of double-entry accounting reports. You can also run business health reports, and leverage bonus features like mobile mileage tracking. Other features include:

  • Direct debit, credit card, and checkout links
  • Recurring billing, subscriptions, and retainers
  • Financial and accounting reports
  • Mobile apps for Android and iOS
  • VAT return filing

You can connect Freshbooks to Shopify via an integration with Zapier, or by using the Freshbooks API. This essentially allows you to sync Shopify customer data, automate order processing, and generate invoices automatically via Freshbooks.


There are four pricing packages available for Freshbooks, depending on the functionality you need. Options include:

  • Lite: £3.50 per month: Supports up to 5 billable clients, unlimited expenses tracking, sales and tax reports, android and iOS apps, and VAT return filing.
  • Plus: £5.70 per month: All of the features of Lite with 50 billable clients, automatic receipt data capture, business health reports, double-entry accounting, accountant invites, and mobile mileage tracking.
  • Premium: $9 per month: All the features of Plus, with unlimited invoices for an unlimited amount of clients. You can also track bills and vendor payments, track project profitability, customize email templates, and email signatures.
  • Select: Custom pricing: Comprehensive enterprise services starting with 2 team member accounts, a dedicated account manager, migration support, custom onboarding, and personalized branding for client emails.


  • Extensive billing and accounting features
  • Access to regulated VAT and tax returns
  • Mobile apps for on-the-go tracking
  • Support for inviting your accountant to your system
  • Automated tracking for Shopify payments


  • Advanced features are reserved for more expensive packages
  • Some limitations with customer support

Best for: If you’re already set up with Freshbooks for subscription billing and tracking mileage, then it makes sense to add the service to Shopify too. This service is also excellent for accessing VAT returns, and state-of-the-art mobile apps.


Few companies have quite as much impact as QuickBooks in the accounting landscape. The company is well-known for offering a huge range of easy-to-use features, from income and expenses reports to tax deduction tracking, and receipt capturing. You can manage your sales and sales tax in one place, create estimates and invoices for your audience, and even track inventory.

QuickBooks is compliant with the latest tax and VAT regulations, making it ideal for business owners around the world. There’s also the option to connect your accountant to your own accountant, so you can get specialist support. Plus, there are a host of project management tools for teams too. Some of the extra features of QuickBooks include:

  • Contractor and time tracking
  • Project profitability analysis
  • Employee expense tracking
  • Workflow automation and project management tools
  • Batch invoicing and estimate
  • Receipt capturing

QuickBooks is easy to integrate with Shopify thanks to the dedicated app for Shopify users. You can align your Shopify data with QuickBooks in a couple of clicks, and automatically import your sales, order details, and inventories in one place. There’s also access to fee recording, and sales tax management, as well as full summaries of account balances.


Similar to many other accounting apps for Shopify, there are a number of packages available for QuickBooks, intended for different user needs. For instance, options include:

  • Simple start: $25 per month for income and expense tracking, invoices and payments, tax deductions, general reports, receipt capture, cash flow, mileage tracking, estimates and contractor management.
  • Essentials: $50 per month for all the features of Simple Start for up to 3 more users, as well as time tracking and bill management functionality.
  • Plus: $80 per month for all the features of Essentials, for up to 5 users, as well as inventory management, and project profitability tracking.
  • Advanced: $180 per month with all the features of Plus, as well as business analytics, employee expense tracking, customized accounts, batch invoices, dedicated account management, workflow automation, on-demand training and data restoration options

You can also add “guided setup” for your account with a live bookkeeper for $50 per session.


  • Excellent compliant tax and VAT recording services
  • Workflow automation and project management
  • Batch invoices and estimates
  • Exceptional tools for tracking team expenses
  • Support from dedicated bookkeeping specialists


  • Can be difficult to set up for beginners
  • Expensive to access the most advanced features

Best for: If you’re looking for an accounting solution to naturally integrate with your Shopify environment and deliver powerful insights, QuickBooks is a great option. There’s fantastic customer support, service, and onboarding features too.


Xero is another of the world’s better-known accounting solutions, and it’s ideal for your Shopify store. Promising a safe and secure solution for managing your finances, Xero allows users to send quotes and invoices, track bills, and even submit VAT returns. You can access automatic CIS calculations and reports, and bulk reconcile transactions too.

The great thing about Xero is its flexibility. You can access cash flow and business snapshots, experiment with multiple currencies, and even unlock a range of add-ons. For instance, there’s support for project tracking, expense claiming, and payroll. However these features do cost extra.

Other features include:

  • Extensive reporting for your ecommerce business
  • Common accounting tools like balance sheets
  • Investment and financial data tracking
  • Equity reports
  • Bank reconciliation

Owned by Sage, Xero integrates directly with Shopify. The company partners with Shopify to give users an easy way to track data from their ecommerce platform, including cost of goods sold, common financial reports, and balance sheets. You can minimize the need for extra data entry for your online business, and track various sales channels in the same place.


There are four pricing packages available from Xero. However, if you want to access extra features like the ability to submit CIS returns or track projects, there are extra costs. Many add-ons start at £5 per month. Packages include:

  • Starter: £12 per month for quotes and up to 20 invoices, management for 5 bills, reconciliation of bank transactions VAT returns, Hubdoc for bills and receipts, and automatic CIS calculations
  • Standard: £26 per month for all the features of Starter, plus unlimited invoices and quotes, short-term cash flow snapshots, and bulk reconciliation.
  • Premium: £33 per month for all the features of Standard plus multiple currencies
  • Ultimate: $49 per month for everything from premium, payroll for up to 10 people, expenses for 5 people, projects for 5 people, and advanced insights.


  • Scalable support for larger businesses
  • Unlimited users available
  • Easy to access advisor support
  • Real-time bank reconciliation
  • Easy quoting and order process


  • A lot of features require extra expenses
  • Prices can change at any time

Best for: If you’re running a larger business or plan on scaling your company quickly, then Xero could be the ideal choice for you. The best packages are the most expensive, but they’re ideal for bigger companies.

Sage Business Cloud Accounting

Another excellent choice for your Shopify business, Sage Business Cloud Accounting is a suite of accounting and payment management tools. Rather than just offering the accounting basics like most of the solutions from leading accounting professionals, Sage also supports payroll, so you can manage your colleagues too.

Sage makes it simple to create and send sales invoices in a convenient interface. You can track who has to pay you, access automatic bank reconciliation, and run all kinds of reports to get a better understanding of your cash flow. There’s even management for purchase invoices. Other features include:

  • Calculate and submit VAT returns
  • Run advanced reports with custom insights
  • Support up to unlimited users
  • Powerful industry-specific features
  • Highly customizable interface
  • Beautiful visuals for tracking information

There’s a basic Shopify integration for Shopify which allows you to automate data and order processing as quickly as possible. However, you’ll need to use a workaround service if you want to link more of the functionality of Sage with Shopify. There’s no all-in-one integration to track all of your reports and expenses in one place.


Sage is extremely generous with its pricing structure, offering 3 months for free on accounting and payroll with all accounts. After your first three months, you can access:

  • Start: £12 per month for sales invoices, invoice tracking, automatic bank reconciliation, VAT submissions and more for 1 user.
  • Standard: £26 per month for all the features of Start for unlimited users, as well as advanced reports, CIS submissions, quotes and estimates, purchase invoices, and forecasting for cashflow.
  • Plus: £33 per month for all the features of Standard plus multi-currency banking and invoicing, and inventory management.

You can also simply pay for the payroll service from Xero starting at £7 per month for up to 5 employees.


  • Highly customizable interface
  • Fantastic for specific industries
  • AI for memorizing categorization choices
  • Automatic transaction matching to save time
  • Access to accounting and payroll in one place


  • Can be expensive to access all the features
  • The integration with Shopify could be more comprehensive

Best for: Sage is excellent for tracking payroll and accounting in one place, with access to a wide range of tools for cash flow forecasting, auditing, job costing, and setting up automated workflows. You’ll just need to figure out how to connect everything.


Wave is ideal for all kinds of small business, freelancers, and a range of other growing companies. If you want a user-friendly environment to help you minimize the time-consuming tasks of small business accounting, this could be the product for you. Wave helps you to streamline reporting and invoicing, and ensures Shopify store owners can keep a close eye on their finances.

The Wave online accounting tool is great for reducing the hassle of accounting for online stores, with a range of free features like unlimited income and expense tracking, and the ability to add unlimited collaborators and accountants. You can access a full double entry system, generate financial statements at year-end, and track overdue invoices. Other features include:

  • Run multiple businesses from the same connected account
  • Organize income and expenses into different tax categories
  • Track sales tax on income and expenses
  • Invoice in any currency, and send estimates
  • Online payment management for ecommerce sites

You can sync to Wave directly with an account within the Shopify app store. This allows you to keep track of orders automatically in Shopify. There’s only a few clicks required to get everything up and running, and there’s no impact on your store’s speed or performance when you implement the service. You can even manage multiple stores in the same place.


While the Wave accounting service is free to use for basic features, you will need to pay something to link everything to Shopify. Using the Sync to Wave app, you’ll spend around $9.95 per month for basic features, with a dedicated free trial. You can also upgrade to the standard plan for $29.95 per month and the Premium plan for $49.95 per month.

There are also other expenses in the Wave environment depending on the functionality you need. For instance, while accounting and invoicing is free, there are transaction fees for online payments accepted through Wave. Credit card processing starts at 1.4% plus 20p for European cards in the UK, and 2.9% and 20p for non-European cards.


  • Fast and secure data setup with minimal expense
  • PayPal integration available
  • Multiple currencies for invoicing and tracking
  • Personalized invoices and dashboards
  • Multiple businesses supported in one account


  • Expensive Shopify add-on
  • Some limitations on accounting compared to other tools

Best for: Wave is a great choice for beginners and smaller companies looking to keep track of their accounting needs within the Shopify environment. Just make sure you know exactly what you’re paying for before you set up your account.

Zoho Books

If tools like Quickbooks online and Zero aren’t right for you, then you could always try Zoho Books. Zoho is best-known for offering a huge range of dedicated tools for online business, including project management and service solutions. It also allows you to track transactions, link your bank account, and create a wide range of expense reports.

With Zoho Books, you get a convenient accounting system which helps with everything from tracking expense management, to setting up role-based user access for your team members. Zoho’s packages are extremely comprehensive, with a comprehensive client portal for self-service, recurring invoices, and credit notes. You can even track sub-accounts. Other features include:

  • Bank rules and reconciliation
  • Invoice customization and audit trails
  • Customizable reports and payment gateways
  • Online and offline payments
  • Transaction locking

You can integrate Zoho Books with Shopify directly using the “Flow” connection solution within Zoho. This gives you complete access to all kinds of reports and insights without the need for any coding set-up. You’ll be able to track when paid orders are created, and even set up triggers when carts are abandoned with convenient webhooks. There are even solutions for creating streamlined automations for your whole team.


If you make less than £35k per year, you can access the basic features of Zoho Books for free for one accountant and one user. This allows you to manage up to 1,000 invoices, track client information, send multi-lingual invoices and credit notes, and manage expenses or mileage. There’s also bank rules and reconciliation and chart of accounts options.

Other packages include:

  • Standard: £10 per organization per month for up to 3 users and everything in “Free”. You’ll also be able to manage up to 5,000 invoices, create user roles, design project tasks, manage taxes, and create bulk updates for your store.
  • Professional: £20 per organization per month for all the features of Standard plus vendor credits, purchase orders and approval, currency adjustment, stock tracking, journal templates, contextual chat, and timesheets.
  • Premium: £25 per organization per month for everything in Professional plus 3 branches, custom domains, vendor portals, budgeting, custom buttons, validation rules, custom modules, custom reports, and workflow rules.

Add-ons are available for additional branches and users, as well as advanced auto scanning functionality for your books.


  • Excellent for collaboration
  • Affordable pricing packages for beginners
  • Easy to use interface with customizations
  • Purchase orders and approval
  • Stock tracking and journal templates


  • Not as advanced as some accounting solutions
  • Extra users will cost more

Best for: Zoho is ideal for all kinds of collaborative work in Shopify, and it even integrates with a range of other CRM and ERP tools. You can also track your expenses across multiple channels, like offline environments and Amazon.

Choosing the Best Accounting Software for Shopify

Finding the best accounting apps for Shopify often feels like a complex process. However, there are plenty of options out there, particularly if you’re willing to use a connector to bring your apps together. The right tool will allow you to track everything from orders to uploaded excel spreadsheets.

We recommend looking for something that integrates naturally with your existing tools, and comes with a free trial service, so you can test out the functionality before you go all-in with your purchase. Make sure the accounting features are also suitable for your specific industry.


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