Top 5 Best Accounting Software for Amazon Sellers in USA

The best accounting software for Amazon sellers in the US should accurately track sales, FBA fees, refunds, reimbursements, inventory costs, and Amazon settlements. Because Amazon deposits net payouts rather than gross sales, basic bookkeeping tools often fail to show true revenue and profit. 

This blog compares five best accounting software for Amazon sellers. It explains their key features, limitations, integrations, and suitability for different business sizes, helping you choose the right Amazon seller accounting software for accurate reporting, tax preparation, and financial control. 

Amazon Seller Accounting Simplified

Track every fee, reconcile payouts, and understand your true profit

Know More

List of Top 5 Accounting Software for US Amazon Sellers

The best accounting software for Amazon sellers includes A2X, Link My Books, QuickBooks Online, Xero, and Microsoft Dynamics 365. Below, we provide broader overview of financial management capabilities of each amazon accounting software. 

A2X

A2X converts Amazon payout data into summarized entries and sends them to QuickBooks Online, Xero, Sage, or NetSuite. It separates sales, refunds, fees, reserves, and sales tax before matching each settlement with the corresponding bank deposit. This makes A2X particularly useful for US sellers managing high transaction volumes or multiple Amazon marketplaces. However, it must be connected to a general ledger platform. 

QuickBooks Online

QuickBooks Online combines bookkeeping, expense tracking, cash flow reporting, inventory monitoring, and financial reporting within one platform. Its Amazon Seller Connector can import orders, refunds, payouts, taxes, and fees from Seller Central. It is a practical choice for small and midsize US sellers working with ecommerce accountants who commonly use QuickBooks. 

Xero

Xero offers cloud accounting, bank reconciliation, cash flow monitoring, and access to Amazon-focused applications such as A2X. Connected applications can synchronize settlement summaries, sales, inventory data, and expenses. Its flexible app ecosystem suits sellers operating across Amazon, Shopify, Walmart, and other channels. 

Link My Books

Link My Books automates Amazon settlement bookkeeping by categorizing sales, refunds, seller fees, and sales tax before posting entries to QuickBooks Online or Xero. It also matches settlement records with bank deposits. US sellers should note that it records Amazon sales tax data but does not replace state-level sales tax calculation or filing software. 

Microsoft Dynamics 365 Business Central

Microsoft Dynamics 365 Business Central is better suited to established Amazon businesses requiring accounting, purchasing, inventory, order management, and operational reporting in one ERP system. Amazon connectivity generally requires a Microsoft Marketplace application or customized integration, making implementation more involved than other tools for accounting for Amazon sellers. 

How to Choose the Right Accounting Software for Your Amazon Business

Choosing the best accounting software for Amazon sellers requires reviewing Amazon integration, settlement reconciliation, sales tax support, inventory accounting, reporting capabilities, and scalability. The right Amazon seller accounting software should accurately record Amazon fees, refunds, reimbursements, advertising costs, and cost of goods sold without requiring excessive manual adjustments.  

Check Amazon Integration and Settlement Reconciliation

Select software that connects directly with Amazon Seller Central or works with a reliable connector such as A2X. It should convert settlement data into summarized accounting entries and reconcile deposits with your US business bank account. 

Review Sales Tax and US Compliance Features

Amazon may collect and remit marketplace sales tax in many states, but sellers can still have filing obligations based on economic nexus. Your system should integrate with tools such as Avalara or TaxJar and maintain clear records for federal and state reporting. 

Evaluate Inventory and Cost of Goods Sold Tracking

Accurate inventory accounting is essential for calculating gross profit and taxable income. The software should track purchases, landed costs, inventory adjustments, returns, and cost of goods sold across Amazon FBA and FBM operations. 

Consider Multi-Channel and Multi-Currency Support

Businesses selling through Amazon need consolidated reporting. International sellers should also check currency conversion, exchange-rate adjustments, and marketplace-level profitability reporting. 

Choose Software That Can Scale

A smaller seller may only need automated bookkeeping and monthly reporting. Larger Amazon businesses often require purchase order management, advanced inventory controls, departmental reporting, and integrations with payroll, sales tax, and enterprise resource planning systems. 

Unlock the Full Potential of Your Software with an Expert Accountant

The right Amazon seller accounting software takes the manual grind out of Amazon bookkeeping, but software alone cannot tell you whether your pricing strategy is profitable, whether your sales tax exposure is under control, or whether you are structured efficiently for tax season. Link My Books, QuickBooks, Xero, A2X, and Zoho Books each solve a real problem, but the real value comes from an ecommerce bookkeeper who knows how to configure them correctly for an Amazon business and read what the numbers are telling you. 

Whiz Consulting specializes in ecommerce bookkeeping for US Amazon sellers, from setting up the right software stack and mapping your chart of accounts correctly, to ongoing reconciliation, sales tax support, and CFO-level insights that help you scale with confidence. Instead of struggling with settlement reports at midnight, you get accurate books delivered on schedule by people who actually understand Amazon’s fee structure. Book a free consultation with Whiz Consulting today and find out how much time, and money, expert-managed bookkeeping can put back into your business.