Ever tried making sense of Amazon settlement reports after a long day of fulfilling orders? Most sellers pause for a moment, stare at the numbers, and wonder how anyone is supposed to keep their books accurate at scale. If you’ve ever felt that way, you’re far from alone.
Amazon moves fast, the fees shift constantly, and the data pours in from every direction. Accounting software for Amazon, in pair with Synder’s ability to pull in every order, fee, and payout automatically and match them to your books, can help you regain control and keep your seller account organized without spending your nights matching transactions line by line.
Below is a practical guide to the best accounting software for Amazon sellers in 2026, plus insights that help you choose a setup you can rely on.
TL;DR
- Amazon bookkeeping can become messy because of complex fees, refunds, taxes, and settlement timing.
- QuickBooks Online, Xero, FreshBooks, NetSuite, and Sage Intacct lead the market in 2026.
- Even the best accounting tools leave gaps in Amazon accounting workflows.
- Synder fills those gaps by automatically syncing Amazon orders, fees, refunds, taxes, and payouts into your accounting system.
- With Synder, Amazon sellers get reliable books, easier reconciliation, and correct tax management.
Key features of Amazon seller accounting software
Good Amazon accounting software should make your daily workflow easier. When comparing your options, look for tools that support:
- Complete import of Amazon accounting data
- Accurate handling of Amazon settlement reports
- Inventory management for Amazon with real-time updates
- Amazon sales tax automation so you stay compliant
- Clear tracking of payouts, taxes, and marketplace fees
- Integrations with platforms you already use
Now that you know what matters, let’s explore the solutions themselves.
Top accounting software for Amazon sellers
Five solutions stand out in 2026 for reliability, scalability, and overall usability.
1. QuickBooks Online
QuickBooks Online is one of the most widely used accounting software solutions for small and mid-sized businesses. The platform includes detailed reporting, flexible categorisation, bank feeds, project tracking, and optional inventory features. Accountants in the United States typically know this system well, which simplifies collaboration.
How it supports Amazon sellers
QuickBooks Online provides a reliable environment for handling large numbers of transactions. Amazon accounting involves many different activity types, and QuickBooks can store that information clearly while giving you useful reports for analysis.
Possible limitations
Higher-tier plans are often required for advanced inventory and more detailed tracking. If your Amazon operation grows quickly, you may need to upgrade sooner than expected.
Best for
Small- to mid-sized Amazon sellers who want familiarity, structure, and strong reporting.
2. Xero
Xero offers cloud-based accounting with a clean interface and unlimited users on many plans. Its simple structure and strong reconciliation tools make it a popular option for sellers who prefer clarity and collaboration.
How it supports Amazon sellers
Xero handles high transaction counts with ease and offers strong visibility into cash flow. Amazon sellers often enjoy the automatic bank feed matching and simple reporting.
Possible limitations
Certain features that ecommerce sellers expect may require additional apps. If your Amazon business becomes complex, you may need more integrations.
Best for
Amazon sellers who want simplicity and ease of use without sacrificing the ability to scale.
3. FreshBooks
FreshBooks is a straightforward accounting software solution focused on ease of use. It offers invoicing, expense tracking, time tracking, and simple reporting.
How it supports Amazon sellers
Smaller Amazon sellers who don’t need enterprise features often enjoy FreshBooks because it removes accounting complexity. The interface feels friendly and predictable.
Possible limitations
FreshBooks lacks some ecommerce-specific functionality. As your Amazon transaction volume grows, you may need more advanced features.
Best for
Small Amazon sellers who prefer simple workflows and minimal learning curves.
4. NetSuite
NetSuite is a comprehensive ERP platform with advanced reporting, multi-entity support, deep inventory capabilities, and broad financial controls. It handles complex structures that many growing Amazon sellers eventually need.
How it supports Amazon sellers
NetSuite can process large data volumes without slowing down. Sellers who operate multiple brands or countries often rely on its consolidated reporting and inventory accuracy.
Possible limitations
NetSuite requires a longer implementation time and a higher budget. It’s designed for established Amazon sellers or those planning rapid expansion.
Best for
Large Amazon sellers with high-volume operations, multi-warehouse inventory, and complex financial needs.
5. Sage Intacct
Sage Intacct is a cloud-based ERP software that offers advanced financial management with multi-dimensional reporting, strong automation capabilities, and excellent visibility into financial performance.
How it supports Amazon sellers
Sellers with large SKU counts or multiple entities appreciate Sage Intacct’s depth. It can support detailed financial analysis and real-time decision-making.
Possible limitations
Sage Intacct uses custom pricing and typically fits larger businesses more than small sellers.
Best for
Growing Amazon sellers who rely on deep analytical insights and want to connect multiple business units.
| Software | Key features | Ease of use | Best for |
| QuickBooks Online | Robust reporting, customizable chart of accounts, built-in inventory on higher plans, strong ecosystem of ecommerce integrations | Easy – intuitive for most sellers | Most Amazon sellers |
| Xero | Unlimited users, clean dashboard, fast bank reconciliation, strong app marketplace, simple financial reporting | Very easy – simple and automated | Amazon sellers who want simplicity and automation |
| FreshBooks | Simple expense tracking, intuitive interface, essential financial reports, straightforward invoicing, and billing | Very easy – beginner-friendly | Smaller Amazon sellers with lighter requirements |
| NetSuite | Enterprise-level financial controls, advanced inventory and demand planning, multi-entity consolidation, detailed analytics | Moderate – requires training | High-volume Amazon sellers with complex needs |
| Sage Intacct | Multi-dimensional financial reporting, advanced automation, granular visibility into performance, scalable structure | Moderate – steep learning curve | Amazon sellers who want powerful reporting and scalability |
The limits of traditional accounting software for Amazon workflows and how to tackle them
If you’ve ever tried running Amazon accounting entirely inside one of these accounting platforms, you already know something feels off. The software itself is strong, but the moment you introduce Amazon settlement data, everything becomes harder: numbers don’t line up, fees disappear, refunds show up days after the sale, inventory quantities drift, and more. In other words, a standard accounting tool is fine, but it isn’t built for the kind of real-time and high-volume activity that Amazon creates.
Synder stands out as the solution that brings everything together. It closes the gaps between your Amazon activity and your accounting software, handling the issues that traditional systems can’t manage on their own. The automation is built for ecommerce realities, not generic bookkeeping scenarios, which is why sellers see the difference immediately.
Let’s take a closer look at the key challenges Amazon sellers encounter when relying on standard accounting solutions and how Synder addresses each.
Understanding Amazon settlement data
Amazon settlement reports mix sales, refunds, shipping charges, advertising costs, and a long list of marketplace fees. Traditional accounting software reads this information as one lump of numbers, leaving you with unclear totals and mismatched entries. Sellers often spend hours trying to identify what belongs where, and even then, the result rarely feels complete.
How Synder solves it
Synder imports settlement data directly from your Amazon seller account and breaks it into clear and traceable components. Every part of the transaction arrives in your books already categorized. You see accurate revenue, fees, and adjustments without manual cleanup. This turns confusing reports into structured financial records that make sense immediately.
Tracking fees and refunds accurately
Marketplace fees change often, and refunds rarely arrive on the same day as the sale. Traditional bookkeeping tools struggle with delayed adjustments and unexpected fee variations. These small inconsistencies add up quickly and create unreliable financials.
How Synder solves it
Synder records every Amazon fee, refund, and adjustment at the moment it appears. Nothing goes missing, and nothing depends on manual entry. Your accounting reflects the true flow of money, which protects your margins and removes the guesswork from performance analysis.
Keeping inventory aligned with Amazon activity
Inventory on Amazon can move rapidly. Units sell, return, restock, and adjust in real time. Traditional accounting software doesn’t always update this information automatically, which leads to inaccurate cost tracking and unexpected stock discrepancies.
How Synder solves it
With pre-transaction mode, Synder keeps your inventory activity aligned with Amazon movements. Costs, quantities, and item details stay consistent across both systems. You always know your true stock position and can manage restocking intelligently rather than reacting to surprises.
Handling Amazon tax withheld correctly
Amazon collects and remits sales tax in many states, but the accounting software doesn’t always reflect these tax-withheld amounts correctly. Sellers often find themselves adjusting entries manually, which increases the risk of errors.
How Synder solves it
Synder simplifies Amazon sales tax collection. It imports the exact tax-withheld amounts from each Amazon transaction, including what Amazon collected and remitted on your behalf. It also avoids creating tax liabilities for amounts already withheld by Amazon. Your accounting software receives correct tax details automatically, helping you stay compliant and removing the need for manual cleanup during filings.
Reconciling Amazon payouts with bank deposits
Matching Amazon payouts to the amounts that land in your bank account is one of the most time-consuming parts of Amazon bookkeeping. The numbers often differ because of fees, reserves, and adjustments that occur behind the scenes.
How Synder solves it
Synder connects your Amazon data with your accounting software and your bank feed. Each payout is matched with the transactions that created it, so reconciliation becomes fast and clear. You see exactly what Amazon withheld, what it released, and why the deposit amount looks the way it does.
Keep your Amazon accounting clear and accurate without the manual work. Try Synder free for fifteen days or book a demo to see how automated syncing handles the details for you.
To sum up: When the numbers finally start making sense
Running an Amazon business is rewarding, but the financial side can feel like a puzzle with a few pieces always missing. The moment your books start reflecting reality instead of a rough estimate, everything becomes lighter. You understand your cash flow better. You make decisions without second-guessing. You stop worrying about what might be hiding in the next settlement report.
Synder helps you reach that feeling faster. It brings order to the financial chaos Amazon creates and gives your accounting software the clarity it needs to keep up with you. If you want your books to feel less like work and more like a tool that supports your growth, giving Synder a try is an easy place to start.
