Running an Amazon business is exciting, but it’s 100% a numbers game and becomes even more so as you grow into a more intermediate level of selling. As your business grows, tracking your income, expenses, inventory, and taxes gets more complicated. That’s where accounting software steps in to save the day. The right tools can make or break your ability to stay profitable, compliant, and stress-free.
In this guide, we’re breaking down the best accounting software for Amazon sellers. If you’ve already moved past the beginner stage and are looking to streamline your operations, keep reading. We’ll explore the top platforms, what to look for, and how to choose the right fit for your Amazon FBA or FBM business.
Why You Need Dedicated Accounting Software for Amazon
Unlike running your own store on Shopify or WooCommerce, Amazon comes with a unique set of accounting challenges that make traditional bookkeeping tools insufficient on their own.
Before jumping into software reviews, let’s talk about why you need accounting software tailored for Amazon sellers.
Amazon-Specific Complexities
Selling on Amazon involves unique challenges:
- Marketplace fees and commissions: Amazon takes a cut from every sale through referral fees, FBA fees, and more. Proper accounting software automatically breaks these down so you can see your real profit margins.
- Inventory tracking across fulfillment centers: FBA sellers must manage inventory stored across multiple warehouses. Good software tracks inventory movement and calculates COGS accurately as inventory shifts.
- Sales tax nexus and remittance: You may owe sales tax in multiple states due to FBA warehouse storage. Accounting tools with sales tax tracking can help you stay compliant and avoid audits.
- Multi-currency transactions (for international sellers): If you sell internationally, Amazon converts currencies for you, but it doesn’t always do so in as detailed and thorough a way as some sellers may prefer. Dedicated tools track exchange rates and fees so your books stay accurate.
- Settlement reports every two weeks (not daily): Amazon pays sellers every two weeks with lump-sum payouts that include fees and adjustments. Accounting software breaks down these settlements to make reconciliation easy.
Generic bookkeeping tools just don’t cut it when you’re dealing with all of the above.
Save Time and Avoid Mistakes
Automated accounting software that integrates directly with Amazon reduces human error and helps you save hours of manual data entry. Here’s how software tailored for Amazon sellers helps streamline your finances and makes your CPA’s life easier during tax season:
- Reduce manual data entry: Automation pulls data directly from Seller Central, cutting hours of manual input and reducing the chance of mistakes.
- Improve accuracy and consistency: Returns, fees, and promotions are tricky to track. Good software categorizes them properly to keep your books clean.
- Make tax time easier: With organized, accurate records, preparing taxes becomes far less stressful. Some tools even support quarterly estimated taxes or integrate with your CPA’s system.
- Gain real insights into profitability: More sales don’t always mean more profit. Accounting software shows you exactly what you’re earning after all costs and fees.
- Scale with confidence: As your business grows, so do your accounting needs. Dedicated software supports multiple sales channels, larger inventories, and more complex operations.
What to Look for in Amazon Seller Accounting Software
Not all accounting software is built with Amazon sellers in mind, and choosing the wrong one can cost you time, money, and accuracy. As your business grows, your accounting system should not only keep up but help you work smarter.
Here are the key features you should look for when choosing the right tool for your Amazon business:
Seamless Amazon Integration
Your accounting software should connect directly to Amazon Seller Central and automatically pull in your transactional data. This includes order details, refunds, shipping income, and fees.
Ideally, the integration happens in real-time or on a regular schedule, so you’re always working with up-to-date information. If you sell on more than one Amazon marketplace (e.g., Amazon US and Amazon UK), make sure the software can handle multiple marketplaces and currencies without requiring separate accounts.
Why it matters:
Manual data entry is slow, error-prone, and completely unnecessary with the right automation. A native Amazon integration ensures your financials are accurate and current, making reporting and reconciliation much easier.
FBA Inventory Tracking
If you use Fulfillment by Amazon (FBA), your inventory is constantly moving between fulfillment centers and customers, and that’s a nightmare to track without the right system. The software you choose should be able to:
- Track inventory levels in real-time
- Account for inventory costs (COGS) correctly
- Handle lost, damaged, and returned inventory
- Factor in FBA storage and fulfillment fees
Some tools even allow you to forecast inventory needs based on sales velocity.
Why it matters:
Inventory is one of your biggest assets and expenses. Without accurate tracking, it’s impossible to know your true profit margins or plan for restocks effectively.
Marketplace Fee Reconciliation
Amazon’s fee structure for sellers is notoriously complicated. There are referral fees, FBA fees, storage fees, refund adjustments, advertising costs, and more. These charges can appear in various places within your Amazon reports, making it easy to miss or miscategorize them.
Your accounting software should automatically extract, categorize, and allocate these fees correctly, ensuring every dollar is accounted for.
Why it matters:
Without fee reconciliation, your profit reports may look artificially inflated. Understanding your actual costs helps you make smarter decisions about pricing, advertising, and profitability.
Sales Tax Compliance
Thanks to changes in U.S. tax laws, Amazon sellers are responsible for collecting and remitting sales tax in any state where they have economic nexus. If you use FBA, just having inventory stored in a state can trigger tax obligations.
The best accounting software for Amazon sellers will:
- Track where you have nexus
- Break out taxable vs. non-taxable sales
- Integrate with tax tools like TaxJar or Avalara
- Generate reports for each jurisdiction
Some solutions even automate your filings.
Why it matters:
Sales tax compliance isn’t optional. Falling behind can lead to penalties, audits, and serious financial headaches. Automation can save you both time and legal risk.
Multi-Channel Capability
Many Amazon sellers expand to platforms like Shopify, Walmart, Etsy, or eBay to diversify their income. If that’s part of your growth strategy, look for accounting software that can handle all your sales channels in one place.
The right tool should consolidate:
- Sales and returns from multiple platforms
- Inventory tracking across all channels
- Financial reporting that separates and compares performance
Bonus points if it supports POS systems or wholesale orders as well.
Why it matters:
As you scale, managing separate accounting systems for each channel becomes a logistical nightmare. Centralized accounting ensures consistency and saves time, especially at month-end or tax season.
The Best Accounting Software for Amazon Sellers
There’s no shortage of accounting tools out there, but most aren’t built to handle the unique demands of selling on Amazon. Below, we’ve curated a list of the top platforms used by advanced Amazon sellers. These tools range from plug-and-play solutions to customizable systems that grow with your business.
Whether you’re looking for hands-off automation, detailed profit tracking, or scalable bookkeeping, there’s an option here that can meet your needs:
1. A2X
Best for: Seamless Amazon-to-Xero/QuickBooks integration
A2X is often regarded as the gold standard in Amazon seller accounting software. It connects your Amazon account with your accounting software (like QuickBooks or Xero) and translates Amazon’s settlement data into clean, easy-to-understand journal entries.
Key Features:
- Automatically fetches Amazon settlements
- Breaks down sales, fees, refunds, and shipping
- Matches deposits with bank feeds in QuickBooks/Xero
- Handles multi-marketplace and multi-currency
Pros:
- Excellent accuracy
- Easy reconciliation
- Great customer support
Cons:
- No built-in invoicing or inventory tracking
- Must be used with QuickBooks or Xero
Price: Starts at $19/month
2. QuickBooks Online (with A2X)
Best for: Sellers wanting full-featured small business accounting
When paired with A2X, QuickBooks Online becomes a powerful solution for Amazon sellers. While not built specifically for Amazon, its flexibility and integrations make it ideal for sellers scaling beyond spreadsheets.
Key Features:
- Robust chart of accounts
- Invoicing, bills, and payroll options
- Financial reporting and forecasting tools
- Integrates with A2X, TaxJar, Shopify, and more
Pros:
- Well-known and trusted
- Extensive integrations
- CPA-friendly
Cons:
- Steeper learning curve
- Requires A2X for Amazon automation
Price: From $30/month (A2X not included)
3. Xero (with A2X)
Best for: Cloud-based, global-friendly accounting
Xero is similar to QuickBooks Online but offers a cleaner interface and more global functionality, including built-in currency conversion. It’s ideal for Amazon sellers outside the U.S. or those who want an alternative to QuickBooks.
Key Features:
- Bank reconciliation
- Payroll, invoicing, and expense tracking
- Inventory management (basic)
- Integrates with A2X and Gusto
Pros:
- Intuitive UI
- Strong international support
- Unlimited users on some plans
Cons:
- Limited U.S. support compared to QuickBooks
- Also requires A2X for Amazon automation
Price: Starts at $15/month (plus A2X subscription)
4. GoDaddy Online Bookkeeping (formerly Outright)
Best for: Solo sellers needing simplicity
If you’re running a smaller operation or side hustle, GoDaddy Online Bookkeeping is a solid, low-cost option. It directly connects to Amazon and PayPal and is user-friendly even for non-accountants.
Key Features:
- Connects to Amazon and PayPal
- Automatic categorization of transactions
- Quarterly estimated tax calculations
- Basic profit & loss reporting
Pros:
- Very easy to use
- Affordable
- Amazon integration built-in
Cons:
- Lacks advanced features
- No multi-user support
- Not ideal for scaling businesses
Price: $4.99/month
5. Sellerboard
Best for: Amazon FBA sellers wanting detailed profitability tracking
Sellerboard is technically more of a profit analytics tool than a full-blown Amazon FBA accounting software, but its data exports and integration options make it useful for financial reporting. If you want to go a step further in analyzing how reviews impact your revenue, try combining Sellerboard with a tool for checking Amazon reviews to track and identify issues alongside your profitability metrics.
Key Features:
- Real-time profit tracking
- Tracks refunds, PPC costs, returns
- Inventory forecasting
- Exportable financial reports
Pros:
- Great dashboard insights
- Strong FBA focus
- Includes PPC tracking
Cons:
- Not a full accounting system
- May require pairing with other software
Price: From $19/month
6. Bench Accounting
Best for: Hands-off bookkeeping with human support
Bench offers a fully managed bookkeeping service, including a team of real humans who categorize and reconcile your transactions each month. They also offer tax filing services.
Key Features:
- Dedicated bookkeeper
- Monthly financial reports
- Year-end tax filing (with Bench Tax add-on)
- Can integrate Amazon data with help
Pros:
- Very hands-off
- Human support
- Great for non-financial founders
Cons:
- More expensive
- Less customizable than DIY options
Price: Starts at $299/month
Honorable Mentions
Not every Amazon seller needs all the bells and whistles found in premium software. Some may prefer to start with more general accounting platforms, either because they’re still testing the waters, want to save on monthly expenses, or have a trusted accountant handling custom configurations.
While these tools aren’t built specifically for Amazon, they can still get the job done with the right setup. If you’re willing to roll up your sleeves and customize your workflows, these honorable mentions might be worth exploring.
Wave Accounting
Best for: Budget-conscious solo sellers or very small businesses
Wave Accounting is a completely free accounting tool that’s surprisingly capable for what it offers. You get features like income and expense tracking, invoicing, and basic reporting, all wrapped in a clean interface.
However, the catch is that Wave does not offer built-in Amazon integrations. You’ll have to manually import transaction data or use third-party tools (like Zapier or CSV uploads) to bridge the gap. This can be time-consuming and potentially error-prone if you’re not careful.
That said, if you’re a small, U.S.-based Amazon seller with relatively simple operations and don’t need advanced automation, Wave can be a smart starting point.
Pros:
- Completely free to use
- Easy-to-navigate dashboard
- Decent reporting for basic needs
Cons:
- No direct Amazon integration
- Limited scalability
- No inventory or COGS tracking
Zoho Books
Best for: Tech-savvy sellers looking for a customizable, all-in-one platform
Zoho Books is part of the larger Zoho ecosystem, which includes CRM, inventory, and email marketing tools. The platform itself is very capable and feature-rich, offering everything from automated workflows to multi-currency support.
While Zoho Books does not have a plug-and-play integration with Amazon out of the box, you can use third-party connectors or custom API integrations to feed Amazon sales data into the system. This flexibility makes Zoho a potential option for sellers with access to development resources or who are already using other Zoho tools.
It’s particularly appealing for international sellers or those managing multiple sales channels in addition to Amazon.
Pros:
- Affordable pricing with rich features
- Supports automation and customization
- Part of a larger suite of business tools
Cons:
- Requires technical setup for Amazon
- May be overwhelming for non-tech users
- Not widely used in the Amazon seller community (less support)
Conclusion
As your Amazon business scales, proper accounting becomes non-negotiable. Using the right accounting software for Amazon sellers can save you hours, reduce errors, and give you a clearer view of your profitability.
Whether you choose a fully integrated system like QuickBooks with A2X, a managed solution like Bench, or a lightweight tool like GoDaddy, make sure it aligns with your workflow, growth plans, and budget.
Don’t wait until tax season to get your books in order. The sooner you get set up with proper Amazon FBA accounting software, the more time you’ll have to focus on what matters: growing your business.
