Running an Amazon business may look simple from the outside—list your products, make sales, and watch revenue grow. But behind the scenes, accounting for Amazon sellers is far from straightforward. Every transaction goes through multiple stages: Amazon fees, fulfillment costs, refunds, advertising charges, and taxes. Without the right accounting software for Amazon sellers, it’s nearly impossible to know your real profit.
Amazon doesn’t just pay you your total sales; it sends net settlements after subtracting all fees and adjustments. That means your bank statement never shows the full financial picture of your store. Good Amazon FBA accounting software automatically imports all sales data, breaks down fees, calculates VAT or sales tax, and matches settlements perfectly with your bank deposits.
Manual spreadsheets or generic bookkeeping tools can’t keep up with this complexity. They miss fees, miscalculate taxes, and cause errors that grow as your store scales. Modern Amazon accounting tools—like Xero for Amazon sellers, QuickBooks Online, or Link My Books—connect directly to your Amazon account and give you real-time insights into profitability and cash flow.
If you want accurate reports, smoother tax filing, and full control over your eCommerce finances, choosing the right accounting software for Amazon sellers is the smartest business move you can make.
Why Amazon Sellers Need Dedicated Accounting Software
Selling on Amazon isn’t like running a regular online store. Every sale goes through Amazon’s system — with platform fees, FBA costs, advertising expenses, and multi-country taxes all mixed in. Managing this manually can lead to mistakes and missed profits. That’s why using the right accounting software is so important for Amazon sellers.
Unlike general bookkeeping tools, accounting software for Amazon sellers which is designed to handle Amazon’s unique structure. It automatically imports sales, refunds, and fees directly from your Seller Central account, giving you an accurate overview of your finances. You can see how much you earn, how much Amazon takes, and how much tax you owe — all in one place.
The best Amazon FBA accounting software also helps with inventory tracking, VAT calculations, and profit reports by product or marketplace. This level of automation not only saves time but also ensures your financial data is accurate every single day.
Whether you’re managing Amazon FBA or FBM, specialized Amazon accounting tools keep your business organized, compliant, and ready to scale confidently.
Key Features to Look for in Accounting Software for Amazon Sellers
Choosing the best accounting software for Amazon sellers means understanding which features truly matter. Not every accounting tool can handle the complexity of Amazon’s transaction structure, so it’s important to pick one built for eCommerce sellers. Below are the most essential features to look for when selecting Amazon FBA accounting software.
1. Automatic Data Sync
The right Amazon FBA accounting software automatically syncs your sales, refunds, and fees from Amazon. This saves hours of manual data entry and reduces the risk of errors.
2. Fee and Expense Tracking
Amazon deducts multiple fees from every order. Good accounting software for Amazon sellers breaks down these costs so you can clearly see your net profit.
3. Multi-Currency and Tax Support
If you sell across regions, your Amazon accounting tools should support multi-currency transactions and automatically calculate VAT or sales tax.
4. Inventory and Cost of Goods Sold (COGS) Tracking
Advanced accounting software for Amazon sellers tracks stock levels, purchase costs, and profit margins in real time.
5. Integration with Tools like Xero or QuickBooks
Seamless integration ensures your Amazon FBA accounting software connects perfectly with your preferred accounting platform for smooth financial reporting.
Top Accounting Software for Amazon Sellers
When you’re looking for the best accounting software for Amazon sellers, it pays to compare the leading options. Below are top tools that fit Amazon businesses — with their strengths, ideal scenarios, and key features.
4.1 Xero for Amazon Sellers
Xero offers excellent functionality for e‑commerce sellers. With Amazon‑specific integrations and inventory add‑ons, it becomes a solid choice for those using Amazon FBA or FBM. Xero for Amazon sellers allows multi‑currency accounting and integrates with Amazon sales through apps.
Why choose Xero?
- It’s designed for cloud accounting, making collaboration with your accountant easy.
- Supports marketplace reconciliation and inventory tracking.
- Ideal for UK/EU and international sellers who want robust software.
4.2 QuickBooks Online for Amazon Sellers
QuickBooks Online often gets top marks as accounting software for Amazon sellers. It’s a strong pick for Amazon FBA businesses because of its reporting, class tracking, and integrations.
Key strengths:
- Familiar interface for many accountants.
- Good ecosystem of apps and integrations (including Amazon connectors).
- Particularly suited if you sell in the US or need US tax reporting.
4.3 A2X – The Connector Tool
Although not strictly accounting software, A2X is nearly essential when using accounting software. It automates Amazon settlement data, turning complex reports into clean journal entries.
Highlights:
- Maps Amazon sales, fees, refunds, and taxes automatically.
- Integrates directly with Xero or QuickBooks, enhancing your Amazon accounting software.
- Trusted by thousands of eCommerce businesses.
4.4 Other Notable Options
Other tools to consider when looking for accounting software for Amazon sellers include:
- Link My Books – simpler Amazon‑to‑accounting connector for UK/EU sellers.
- Zoho Books – good for smaller sellers or multilingual/multicurrency needs.
- Sage Business Cloud – works with Amazon connectors like A2X to support settlement reconciliation.
4.5 Comparison Table
| Software | Best For | Key Feature for Amazon Sellers |
| Xero | UK/EU sellers, multi‑currency | Strong integrations, inventory support |
| QuickBooks Online | US sellers, traditional bookkeeping | Familiar for accountants, strong reporting |
| A2X (as connector) | All sellers seeking automation | Automates mapping Amazon to accounting software |
| Link My Books / Zoho / Sage | Smaller sellers / niche needs | Cost‑effective or regional alternatives |
Integrating Amazon with Accounting Software
One of the most important steps for Amazon sellers is connecting your store to the right accounting software. Without proper integration, even the best accounting tools can’t give you accurate financial insights.
Integration ensures your Amazon sales, fees, refunds, and taxes automatically flow into your accounting system. For example, using A2X or Link My Books alongside Xero or QuickBooks Online converts complex Amazon settlements into clean, organized entries. This means your Amazon accounting tools reflect the true profit per product, monthly revenue, and expense breakdown without manual input.
Automating data transfer also helps with multi-currency transactions and VAT or sales tax calculations. Your Amazon FBA accounting software can automatically handle different currencies from Amazon US, UK, or EU marketplaces, calculate exchange rates, and ensure compliance with regional tax rules.
Proper integration saves Amazon sellers hours of weekly bookkeeping and minimizes errors. With the right setup, your accounting software it produces accurate monthly reports, real-time insights into profitability, and a reliable audit trail for tax authorities.
For Amazon sellers who want peace of mind, a professional setup by experts like eSeller Accountant ensures your accounting software works perfectly from day one, so you can focus on growing your Amazon business.
⚠️ Common Mistakes Sellers Make When Choosing Accounting Software for Amazon Sellers
Many Amazon sellers pick accounting tools without fully understanding the complexity of marketplace transactions. Choosing the wrong accounting software for Amazon sellers can lead to errors, wasted time, and even tax issues. Here are the most common mistakes to avoid:
1. Ignoring Amazon Integration
Selecting Amazon FBA accounting software that doesn’t integrate with Amazon settlements leads to hours of manual data entry. Without integration, your software can’t automatically track fees, refunds, or multi-currency payments accurately.
2. Overlooking Tax and VAT Features
Amazon sellers often need VAT (UK/EU) or sales tax (US) support. Choosing right accounting software for Amazon sellers without tax automation can result in compliance problems and late filing penalties.
3. Relying on Generic Bookkeeping Tools
Spreadsheet-based or generic accounting software might work for simple businesses, but they can’t handle FBA, FBM, or multi-marketplace complexities. Using proper Amazon accounting tools ensures accurate reconciliation of orders, fees, and returns.
4. Not Considering Inventory and COGS
Failing to track inventory costs properly can inflate profits on paper. The right Amazon FBA accounting software calculates cost of goods sold (COGS) and tracks stock across multiple warehouses automatically.
5. Choosing Based on Price Alone
The cheapest tool may not handle Amazon’s complexity. instead of investing in robust and choosing the right accounting software for Amazon sellers saves money in the long run by preventing errors, improving reporting, and keeping you tax-compliant.
Why Choose eSeller Accountant for Amazon Accounting Setup
Selecting the right accounting software for Amazon sellers is just the first step. Setting it up correctly is equally important. That’s where eSeller Accountant comes in — helping Amazon sellers get their accounting systems fully integrated, automated, and accurate from day one.
1. Marketplace Expertise
Our team understands Amazon’s unique fee structure, FBA complexities, and settlement reports. We ensure your Amazon accounting tools accurately track every sale, refund, and expense.
2. Seamless Software Integration
We specialize in integrating accounting software for Amazon sellers like Xero and QuickBooks Online with Amazon connectors such as A2X and Link My Books. This setup automates data flow, reduces manual entry, and ensures real-time financial insights.
3. VAT & Sales Tax Compliance
Whether you sell in the UK, EU, or US, our experts make sure your Amazon FBA accounting software handles VAT, OSS, or US sales tax correctly, keeping your business compliant with tax authorities.
4. Clear Reporting & Insights
We configure your accounting software for Amazon sellers to generate reports that show profits by SKU, marketplace, or ad campaign. This clarity helps you make smarter decisions and grow your Amazon business.
5. Ongoing Support
From monthly reconciliations to audits, our team ensures your Amazon accounting tools continue running smoothly, giving you peace of mind and freeing you to focus on scaling your store.
CTA: Book a free consultation with eSeller Accountant today to set up your accounting software for Amazon sellers correctly and start optimizing your profits.
❓FAQs for Amazon Sellers
1. What accounting software is best for Amazon sellers?
The best accounting software for Amazon sellers depends on your business size and marketplace. Popular options include Xero, QuickBooks Online, and connectors like A2X or Link My Books to automatically track Amazon sales, fees, and refunds.
2. Do I need a connector like A2X for my Amazon store?
Yes. Amazon settlements include multiple fees, refunds, and multi-currency pay-outs. Using Amazon accounting tools like A2X ensures your Amazon records all transactions automatically and accurately.
3. Can accounting software for Amazon sellers handle VAT or sales tax?
Absolutely. Modern accounting software for Amazon sellers can calculate VAT for UK/EU sellers and sales tax for US sellers, keeping you compliant with tax regulations without manual calculations.
4. How often should I reconcile my Amazon accounts?
It depends on your sales volume. For most sellers, Amazon accounting software should be reconciled monthly. High-volume sellers may prefer weekly reconciliation to monitor cash flow, profit margins, and fees.
5. Can I track inventory and COGS with Amazon accounting software?
Yes. Tools like Xero for Amazon sellers or QuickBooks Online integrated with connectors allow you to track inventory, calculate cost of goods sold (COGS), and generate accurate profit reports by SKU or marketplace.
6. Is manual bookkeeping enough for Amazon sellers?
Manual spreadsheets are prone to errors, especially as your store grows. Using Amazon FBA accounting software ensures automatic data sync, reduces mistakes, and provides real-time financial insights.
✅Optimize Your Amazon Business with the Right Accounting Software
Choosing the right accounting software for Amazon sellers is essential for running a profitable, compliant, and scalable Amazon business. The right software automates complex Amazon transactions, tracks inventory, calculates VAT or sales tax, and produces accurate profit reports — saving time and reducing errors.
However, selecting the software alone isn’t enough. Proper setup, integration, and ongoing management are critical to ensure your Amazon accounting tools deliver real insights. That’s where professional support from eSeller Accountant makes a difference. Our team specializes in connecting Amazon stores to Xero, QuickBooks Online, A2X, and Link My Books, configuring reports, and keeping your accounting software for Amazon sellers accurate month after month.
If you want to simplify bookkeeping, stay tax-compliant, and gain a clear view of your Amazon business’s profitability, contact us today. Let us help you get your accounting software running efficiently so you can focus on growing your store.
