The Best Ecommerce Accounting Tools for 2025
In this blog, we’ll explore the best ecommerce accounting tools for 2025, covering everything from bookkeeping and invoicing to tax compliance and inventory management.
Running an ecommerce business can be an exciting and profitable venture, but managing your finances effectively is key to long-term success.
With multiple sales channels, inventory to track, and VAT compliance to navigate, ecommerce accounting can quickly become overwhelming. Thankfully, 2025 offers an impressive lineup of tools that streamline accounting processes, automate repetitive tasks, and give you the insights needed to grow your business.
1. Xero: The All-in-One Accounting Powerhouse
Xero remains a favourite among ecommerce businesses for its user-friendly interface and robust features. As a cloud-based platform, it integrates seamlessly with sales channels like Shopify, Amazon, and eBay, giving you real-time insights into your financial performance.
Key Features for Ecommerce Businesses:
Automated bank reconciliations for faster bookkeeping.
Seamless integration with third-party apps like A2X and DEXT.
Real-time profit and loss reports to monitor your business health.
Multi-currency support for international sellers.
With its scalability and flexibility, Xero is ideal for businesses of all sizes, whether you’re just starting out or managing high transaction volumes.
2. QuickBooks Online: A Tried-and-True Favourite
QuickBooks Online is another top contender for ecommerce businesses in 2025. Known for its wide range of features, it simplifies financial management and integrates easily with most ecommerce platforms.
Key Features for Ecommerce Businesses:
Automatically track income and expenses across multiple platforms.
Invoice generation and payment tracking in one place.
Integration with apps like Shopify, Amazon, and WooCommerce.
Powerful reporting tools to identify trends and make informed decisions.
QuickBooks Online’s intuitive design and powerful analytics make it a reliable choice for ecommerce sellers looking to streamline their accounting processes.
3. A2X: The Integration Expert
If you’re selling on platforms like Shopify, Amazon, or eBay, A2X is a must-have tool. It connects your ecommerce platform to accounting software like Xero and QuickBooks, automating the process of reconciling sales and fees.
Key Features for Ecommerce Businesses:
Automatically imports and organises transaction data from your sales channels.
Reconciles payouts with bank deposits for accurate bookkeeping.
Tracks VAT and sales tax, helping with compliance.
Customisable reporting to get insights specific to your ecommerce business.
A2X saves time by eliminating manual data entry and ensures your books are always accurate.
4. DEXT (Formerly Receipt Bank): Simplifying Expense Management
DEXT is a powerful tool for automating expense tracking and data entry. It’s particularly useful for ecommerce businesses with high volumes of receipts, invoices, and supplier payments.
Key Features for Ecommerce Businesses:
Captures and processes receipts and invoices with a simple photo or upload.
Integrates with Xero, QuickBooks, and other accounting software.
Automates data entry, saving hours of manual work.
Tracks multi-currency expenses for international sellers.
DEXT is perfect for keeping on top of your expenses, ensuring your cash flow is accurate and well-managed.
5. Hubdoc: Your Paperless Filing Cabinet
Hubdoc is an excellent tool for ecommerce businesses that want to go paperless while staying organised. It automatically pulls financial documents from your accounts, including invoices, bank statements, and receipts, saving you hours of work.
Key Features for Ecommerce Businesses:
Centralised document storage for easy access.
Automatic data extraction and syncing with accounting software.
Receipt and invoice tracking to streamline bookkeeping.
Simplifies preparation for tax season.
For businesses looking to digitise their finances, Hubdoc offers a simple and efficient solution.
6. Xero Analytics Plus: Advanced Reporting for Growth
For ecommerce businesses aiming to scale, Xero Analytics Plus is a game-changer. This add-on provides in-depth financial insights that go beyond standard reporting tools.
Key Features for Ecommerce Businesses:
Forecast cash flow to make informed decisions.
Analyse business performance with customisable dashboards.
Plan for growth with financial insights tailored to your goals.
When combined with Xero’s core features, Analytics Plus gives you a complete view of your ecommerce finances.
7. TaxJar: Simplifying Sales Tax Compliance
Sales tax compliance can be one of the biggest headaches for ecommerce businesses, especially if you sell in multiple states or countries. TaxJar automates the entire process, ensuring you never miss a deadline.
Key Features for Ecommerce Businesses:
Automatically calculates sales tax for every transaction.
Tracks tax liabilities by region, helping with compliance.
Generates tax reports and files returns on your behalf.
TaxJar is essential for businesses looking to stay compliant with sales tax regulations, saving time and reducing the risk of errors.
8. Fathom: Financial Analysis Made Easy
Fathom is a powerful reporting and analysis tool designed to help ecommerce businesses understand their financial data. It integrates with Xero and QuickBooks to turn complex numbers into clear, actionable insights.
Key Features for Ecommerce Businesses:
Customisable dashboards to track KPIs.
Scenario planning to test financial strategies.
In-depth performance reporting for smarter decision-making.
For ecommerce sellers looking to plan for growth, Fathom provides the tools you need to stay ahead.
Why Choose Finance Box for Your Ecommerce Accounting Needs?
At Finance Box, we specialize in ecommerce accounting and understand the unique challenges that online businesses face. With expertise in tools like Xero, DEXT, A2X, and Hubdoc, we help you:
Automate your bookkeeping and streamline processes.
Stay VAT-compliant across the UK and EU.
Gain real-time insights to grow your business.
Our team of ecommerce accounting experts ensures your financials are accurate, compliant, and easy to manage, so you can focus on scaling your business.
Empower Your Business with the Right Tools
The right accounting tools can make all the difference for ecommerce businesses in 2025. By integrating platforms like Xero, A2X, and DEXT into your workflow, you’ll save time, reduce errors, and gain the financial clarity needed to succeed in a competitive market.
Not sure where to start? Contact Finance Box today, and let’s talk about how we can help you implement the best ecommerce accounting tools for your business.