7 Best Accounting Software for E-commerce Sellers (2026)
Don't waste money on the wrong tools. We analyzed the top Accounting Software to help you find the perfect match for e-commerce sellers.
Xero
The e-commerce favorite. Its inventory management is superior to QuickBooks, allowing you to track stock levels and Cost of Goods Sold (COGS) accurately across multiple channels.
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Runner Ups
QuickBooks Online
Scaling BrandsThe industry standard. If you plan to sell your business or seek a loan, you need QBO. Every accountant knows it, and it handles complex sales tax nexus issues better than most.
- Universally accepted by accountants
- Powerful sales tax center
- Massive integration library
- Inventory features are clunky
- Price hikes are common
Starting at
$30/mo
A2X
Amazon/Shopify SyncThe missing link. A2X isn't a ledger, but a connector. It takes your messy Amazon/Shopify payouts and posts them to Xero/QBO as clean, reconciled journal entries. Essential.
- Reconciles payouts to the penny
- Separates sales, fees, and refunds
- Saves hours of manual data entry
- Requires Xero or QBO
- Another subscription cost
Starting at
$19/mo
Link My Books
Marketplace SellersA cheaper, highly rated alternative to A2X. It automates the bookkeeping for Amazon, eBay, and Etsy sellers, ensuring your tax returns match what you actually received in the bank.
- Excellent transparent pricing
- Guided setup for non-accountants
- Supports TikTok Shop
- Fewer integrations than A2X
- Focus is purely marketplaces
Starting at
$17/mo
TaxJar
Sales Tax AutomationCrucial for compliance. Once you cross economic nexus thresholds in multiple states, TaxJar automates the filing of sales tax returns so you don't go to jail.
- Auto-files returns in every state
- Tracks economic nexus progress
- Reliable 'rooftop' accuracy
- Expensive for low volume
- Support can be automated
Starting at
$19/mo
Frequently Asked Questions
Common questions about choosing the right software.
We analyze dozens of data points including pricing, feature sets, user reviews from trusted platforms (like G2 and Capterra), and real-world performance. Our "Top Pick" balances raw power with value for money.
Yes, software pricing is dynamic. While we update our database regularly (Last update: February 2026), we recommend clicking the "Check Price" button to see the most current live offers.
Yes! We may earn a small commission if you purchase through our links, but this comes at no extra cost to you. This supports our research team.