10 Best Ecommerce Accounting Software
Ecommerce accounting is no easy task – even for experienced accountants.
You’re often dealing with a high volume of orders across multiple sales channels, which creates unique challenges. An efficient eCommerce accounting software system is essential for accurate financial recording.
But with so many software options available, where do you even start?
This article dives into the best eCommerce accounting software available for businesses. We’ve analysed customer reviews, tested the software functionality, and considered the reliability of each software vendor to bring you the top 10 tools for 2025.
Here are the results.
How we decided the 10 best eCommerce accounting systems
Determining the best eCommerce accounting software requires a holistic look at the pros and cons of each product.
Our research process considered the key challenges of eCommerce accounting and how effectively the software solves them. We’ve also weighed up important buying factors such as cost, user experience, customer support, and product limitations.
The eCommerce accounting software features we'll looking for include:
- Automated reconciliation
- Real-time reporting
- Ecommerce integrations
- Invoicing and payment processing
- Capacity to scale
- Multi-currency transactions
- Tax management
While these features are important, the other factors we mentioned matter too.
Ultimately, the best eCommerce accounting software for you will depend on the immediate and future needs of your business.
10 best eCommerce accounting software in 2025
Based on functionality, reviews, price, and support, here are the 10 best eCommerce accounting software for 2025, in no particular order:
1. A2X
A2X is an eCommerce accounting connector app that sits between cloud accounting software and ecommerce platforms. It downloads your transaction statements from platforms like Shopify and Amazon and then breaks them down into easy-to-reconcile journal summaries that are posted directly into your accounting system.
Why it’s great
A2X helps merchants that sell through online platforms like Amazon, Shopify, Etsy, eBay, and Walmart to streamline the process of categorising and reconciling business transactions.
Because payments from these platforms are distributed in batches, it can be tricky to break them down accurately and efficiently into their individual transactions. This leads to complications when it comes to financial reporting, tax compliance, and reconciliation.
A2X eliminates this problem by automating those breakdowns and integrating your sales channels with QuickBooks Online, Xero, or Sage.
Who it’s best for
A2X is a useful tool for small to medium eCommerce businesses already using one or more of the eCommerce platforms and accounting systems mentioned above. While it has limitations for larger organisations – or those using different software – it is one of the most popular eCommerce accounting tools on the market.
Pros
- Saves you hours with automated bank reconciliation
- Uses the accrual accounting method to give a more accurate picture of your finances
- Connects Amazon, Shopify, Etsy, eBay, and Walmart with QuickBooks Online, Xero, or Sage
Cons and limitations
- Currently only integrates with a handful of business solutions
- Only helps you with one aspect of eCommerce accounting, not a complete finance management system
2. Access Financials
Access Financials is a powerful finance management system that combines cloud-based accounting software with projects, sales processing, purchasing, and operations. Its scalable pricing and robust functionality give growing businesses the freedom to be more productive and efficient in their daily activities.
Why it’s great
Access Financials’ advanced financial management features support multi-company and multi-currency accounting, while further supporting the growth of expanding businesses with multi-dimensional reporting and business insights.
Unlike other options on this list, Access Financials helps medium or complex companies achieve maximum control and financial visibility. Its bespoke flexibility and powerful integrations provide a complete platform for streamlining all your reporting and bookkeeping needs.
Who it’s best for
Access Financials offers a more robust, growth-friendly cloud accounting system than other similar software – making it the perfect choice for complex businesses, medium-sized firms, and not-for-profit organisations.
Pros
- A complete solution for managing all the financial aspects of your business, from project accounting to stock control
- Specifically designed to support the growth needs of complex or scaling businesses
- Comes with dedicated support from over 250 UK-based finance experts
Cons and limitations
- May be too expensive or feature-rich for emerging businesses
- Does not have native integrations with popular eCommerce platforms
3. Xero
Xero is a popular cloud-based accounting software designed for small and fast-growing companies. It helps you improve the accuracy of your financial recording processes and streamline accounting workflows by automating repeatable manual tasks.
Why it’s great
Xero provides a clean, user-friendly interface that offers financial visibility and cost-effective online bookkeeping. Because it’s made to help small and medium businesses better manage their financial data, it comes at a lower price point than similar tools more tailored to large organisations.
Who it’s best for
Small and medium businesses looking to switch from spreadsheet or pen-and-paper accounting systems may find Xero the perfect tool for their ecommerce accounting.
The Xero App Store – Xero’s integration marketplace – offers integrations with hundreds of the world’s most reliable apps and software tools, making it easy to create a single source of truth for all your business data in Xero.
Pros
- Affordable subscription fees that make it a feasible solution for smaller businesses
- Unlimited users and cloud-based software mean you can easily collaborate from anywhere, with anyone in your team
- Integrates with a wide range of third-party tools and plugins to enable a custom user experience
Cons and limitations
- Limited features compared to larger, enterprise accounting software
- Requires additional plugins to import and break down settlements from your ecommerce sales channels
- Xero’s interface lacks a wide range of customisability options as its feature set is mostly predefined
4. QuickBooks Online
QuickBooks Online (QBO) is a cloud-based accounting tool with an estimated 80% market share in the United States. It’s owned by parent company, Intuit, and is the online version of Intuit’s general accounting software QuickBooks.
Why it’s great
QuickBooks Online offers a lot of functionality at a much more affordable price than other similar products. This makes it very popular with freelancers and small organisations. Its reporting suite is also highly touted for its advanced reports and profitability projection functionality.
Who it’s best for
With its low subscription cost and relatively vast feature set, freelancers, small businesses, and contractors may find QuickBooks Online the ideal solution for recording all your retail and ecommerce transactions.
If you’re based in the US, there’s a good chance your accountant will recommend you use QuickBooks Online. However, businesses outside the US might wish to avoid it as Intuit primarily targets US-based customers with its software updates.
Pros
- An affordable, cloud-based system that integrates with lots of third-party tools
- Feature-rich for a low-cost cloud accounting solution
- Easy-to-use interface and a smaller learning curve than large enterprise tools
Cons and limitations
- Some users report frequent system crashes and platform instability
- Requires additional plugins to reconcile individual transactions from ecommerce platform settlements
- Built for small businesses, may not be suitable for large or scaling enterprises with complex eCommerce accounting needs
5. Synder
Synder is an eCommerce accounting software tool that enables multichannel retailers to synchronise data across different systems and track key business metrics in a single, cloud-accessible location.
Why it’s great
Synder solves several common problems for multichannel eCommerce businesses. Its data sync functionality allows you to easily capture and reconcile transactions from all your sales channels.
Meanwhile, the business intelligence features offer real-time insights based on a holistic analysis of your multichannel sales data.
Who it’s best for
Businesses that sell goods across multiple sales channels such as Shopify and Amazon may enjoy the benefits of Synder software – especially if you’re looking for a way to analyse performance across the entire business.
Pros
- Integrates with and syncs data between 25+ eCommerce and accounting platforms
- Create and analyse multichannel KPI reports for data-driven decision-making
- Scalable plan sizes make Synder a practical solution for businesses of nearly all sizes
Cons and limitations
- User interface can be complicated to learn and master
- Can be quite expensive compared to similar products that offer the same functionality
- Does not provide a complete accounting system for ecommerce, and is more useful as a plugin that sits alongside other applications
6. Link My Books
Link My Books is an eCommerce accounting plugin that connects Amazon, Shopify, eBay, Walmart, Etsy, and TikTok with Xero or QuickBooks. It enables merchants to automatically sync platform payouts with their accounting software and break them down into individual transactions.
Why it’s great
Ecommerce platform payouts can be opaque when it comes to line-by-line transactions, and they’re often posted at periods that don’t align with your financial recording. Link My Books saves you time and money by automatically matching payouts with your bank transactions to ensure accurate ecommerce accounting.
Who it’s best for
Ecommerce merchants (and their accountants) already using Xero or QuickBooks Online – especially those selling on alternative platforms like TikTok Shop or Etsy – can save time and money by integrating their accounting software with Link My Books.
Pros
- One of the only tools that integrates TikTok Shop with cloud accounting software
- Greatly loved by its users, with countless 5-star reviews across different rating sites
- Affordable pricing that’s based on the number of orders you process each month
Cons and limitations
- Acts as a connector app; does not provide a full financial management service
- Only suitable for businesses that use one or more of the handful of accounting and eCommerce software that integrate with Link My Books
7. Sage Business Cloud Accounting
Sage Business Cloud Accounting, formerly known as Sage One, is a small business accounting tool that helps you manage cash flow, invoicing, payroll, tax, and reconciliation. It’s designed to automate manual bookkeeping processes and simplify tax management.
Why it’s great
Sage Business Cloud Accounting offers extensive reporting features that allow you to generate regular financial reports and compare financial statements across different periods of time. It’s also highly customisable, allowing you to tailor the software to meet your specific needs.
Who it’s best for
Small businesses with complex accounting needs can benefit from Sage’s accounting software. While certain features may be excessive for simple organisations, or limiting for large organisations, Sage Business Cloud Accounting offers a unique solution for those that sit somewhere in between.
Pros
- Strong, comprehensive reporting functionality for advanced data analysis
- A broader set of features than other small business accounting software
- Integrates with dozens of popular third-party tools and services
Cons and limitations
- It can take a long time to implement and learn to use due to complicated features
- It’s an expensive option for small businesses, yet lacks the necessary features for larger businesses
- Users have reported delays and unsatisfactory experiences with Sage’s customer support program
8. FreshBooks
FreshBooks is a simple, easy-to-use cloud accounting system designed for solo business owners and small, uncomplicated companies. It provides all the basic features small businesses need to automate invoicing, streamline financial reporting, and manage taxes.
Why it’s great
Because FreshBooks is specifically designed for freelancers and simple businesses, it has a reputation for being one of the easiest accounting software tools to learn and use. You can easily access key reports and analytics, integrate with your preferred eCommerce platform, and track project time from the intuitive FreshBooks dashboard.
Who it’s best for
FreshBooks is a good choice for freelancers, solopreneurs, and sole proprietors with basic eCommerce accounting needs. While it lacks the customisability and complexity of similar software products, its easy-to-use interface and affordable pricing make it ideal for solo business owners and simple startups.
Pros
- Intuitive, easy-to-use interface ideal for simple accounting activities
- Very affordable subscription prices compared to similar software
- Comes with practical features like automated invoicing and double-entry reporting
Cons and limitations
- May be unsuitable for large businesses or those with complex accounting needs
- Limited customisation options and dashboard flexibility
- Scaling businesses may need to switch software when their needs outgrow FreshBooks’ capabilities
9. Bench
Bench is a fintech company that provides accounting software and access to in-house advisory services to give businesses total bookkeeping support when they need it. In other words, it offers a combination of digital finance management and real human support to help you tackle all your accounting needs.
Why it’s great
Bench matches you with a team of professional bookkeepers, provides unlimited support, and functions as your accounting software. Unlike other providers on this list, Bench is a complete accounting package that kills two birds with one stone: finding reliable accounting software and finding reliable accountants to manage it.
Who it’s best for
Business owners and brands that are looking for both an accountant and an accounting software platform may enjoy the hands-free bookkeeping Bench offers. Bench also provides year-round support from accounting experts, making it perfect for companies lacking confidence in the accuracy of their financial records.
Pros
- Easy-to-use dashboard that prioritises intuitive user experience
- Unlimited tax advisory services all year round
- Their current free trial offer includes an entire month of complimentary bookkeeping
Cons and limitations
- It’s a proprietary software, which makes it difficult to switch to another provider
- Monthly subscription costs are higher than most other providers (but perhaps lower when accountant fees are added to the comparison)
10. Zoho Books
Zoho Books is an online accounting app that automates your business workflows and offers an end-to-end financial management system for businesses of all sizes – from freelancers to large enterprises.
Why it’s great
Zoho Books offers a free subscription plan with basic accounting features, allowing businesses to move away from spreadsheets regardless of their budget size. The Zoho ecosystem contains 50+ apps that integrate with Zoho Books, enabling you to operate your entire business on one platform.
Who it’s best for
If you’re already using Zoho products, or you’re looking for free accounting software that’s a step up from messy spreadsheets, Zoho Books may be the right solution. As one of the only cloud accounting systems that comes with a free plan, Zoho Books is a good solution for companies with a small (or non-existent) software budget.
Pros
- Free subscription plan available with basic accounting features
- Role-based access that makes it easy to collaborate with employees across the business
- Scalable subscription plans suited to all business sizes and needs
Cons and limitations
- Limited customisation options and an overly complicated reconciliation system
- Users have reported unsatisfactory customer support from the provider
- A lack of advanced accounting features means it may be unsuitable for large or growing businesses
How to choose the best eCommerce accounting software
When shopping for the best eCommerce accounting software, you must consider the specific needs of your business and the problems you need to solve. Additionally, your budget may exclude some options from consideration as ecommerce accounting software costs can largely vary.
For freelancers and new startups, a simple accounting tool that offers basic financial reporting features may be sufficient – at least until you start to scale.
For medium and large enterprises, a more robust solution with advanced accounting features, a system that supports growth, and reliable integrations will help you stay on top of your complex financial responsibilities.
To learn more, check out our guide: How to choose the right accounting software for your business.
Grow your online business with eCommerce accounting software
Access Financials is a versatile finance management system that helps you streamline your ecommerce accounting processes while giving you total control of your finances, operations, and projects.
When you implement our eCommerce accounting software, you’ll get:
- All your financial data securely stored and accessible on the cloud
- Automated eCommerce accounting processes that save you hours
- Dedicated support from 250+ finance experts
- Every feature you need to sustainably scale your business and boost productivity
Are you ready to optimise your eCommerce accounting with Access Financials? Book a free demo of the software today to get started.