5 Best Accounting Software For Amazon Sellers May 2025 (SAVE Time & Money)

Running an Amazon business is exciting, but the accounting side can be a real challenge. Keeping track of fees, taxes, and inventory is often time-consuming and complex. 

Many sellers find themselves spending hours on paperwork instead of growing their business.

The good news?

Accounting software for Amazon sellers can do these jobs for you. 

In this post, we'll explore how the right software can simplify your bookkeeping, save you time, and help avoid costly mistakes.

Best Accounting Software for Amazon Sellers

• Xero with Link My Books
• QuickBooks Online with Link My Books
• Zoho
• Wave
• Sage

Xero is a cloud-based accounting software designed to simplify financial management for small and medium-sized businesses. 

Its user-friendly interface and powerful features in combination with Link My Books have made it a popular choice for Amazon sellers and bookkeepers looking to streamline their operations.

Top Features of Xero

• Easy Bank Matching: Xero automatically matches your Amazon money with your bank account. This keeps your transaction records up-to-date without you having to do it manually.
• VAT Help: Xero follows UK tax rules and lets you send VAT returns right from the app. Coupled with Link My Books ensuring all your Amazon sales have the right tax rates applied, rest assured you won't overpay.
• Works with Many Apps: Xero can connect to over 1,000 other apps, like inventory management or cash flow forecasting apps.
• Learning Materials: Xero gives you lessons, videos, and online classes to help you learn and upgrade your skills.
• Get Certificates: You can take classes to get certificates in using Xero and managing pay for workers. 

Ease-of-Use and Customer Support

Once you get the hang of it, Xero's accounting tools are straightforward, you can generate reports automatically and view them with a single click.

Customer Support:

• 24/7 Online Support: Xero members have access to round-the-clock online support.

However, to automate your Amazon accounting, Xero needs the data from your sales channels. 

While Xero offers essential accounting features, it can be time-consuming and error-prone when managing e-commerce sales without additional tools. 

Here are some key disadvantages

• Manual Data Entry: Manually entering sales data from multiple e-commerce platforms into Xero is time-consuming and prone to errors.
• Complex Transaction Structures: E-commerce transactions often involve various fees, taxes, and refunds, making manual reconciliation challenging.
• Time-Consuming Reconciliations: Matching bank deposits with sales data can be a lengthy and tedious process.
• Lack of Specialized Features: Xero might not have specific features tailored to the unique needs of e-commerce businesses, such as automated fee and tax calculations.

Xero works best with Link My Books. It’s flexible and integrates with all your sales channels, making it ideal for eCommerce businesses that sell on multiple platforms.

Link My Books + Xero = Error-free Accounting 

Amazon selling has a lot of tricky parts. Trying to do all this manually in Xero can take a long time and lead to mistakes.

Link My Books is designed to streamline and enhance your financial management. 

It integrates with popular e-commerce platforms like Amazon, eBay, Shopify, Etsy, and more to automatically import sales data into accounting software such as Xero or QuickBooks. Plus it provides you with financial analytics and industry benchmarking to help you make smarter decisions on how to grow your business profitably.

How Does it Work?

1. Connect your Amazon account to Xero via Link My Books.

2. With each Amazon payout, Link My Books verifies all transactions, ensuring that every order is treated correctly for tax purposes.

3. Link My Books then creates a detailed summary invoice in Xero, itemizing the payout into sales, refunds, and fees, and assigning them to the proper accounts with the correct tax rates.

4. The Xero entry matches effortlessly with the bank deposit in a single click.

Xero Pricing

For UK Customers

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For US Customers

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For AU Customers 

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QuickBooks Online is a cloud-based accounting software trusted by millions of businesses worldwide. The software gives sales updates in real-time, as well as status alerts. 

While it does offer an integration called Amazon Seller Connector by QuickBooks, this integration is often faulty and does not pull your data correctly. 

For Amazon sellers, the real game-changer is pairing QuickBooks with Link My Books.

Link My Books & Quickbooks = Advanced Reporting 

While QuickBooks Online is packed with accounting features, it doesn’t always cover the specific needs of Amazon sellers, who face complex tax obligations, varying fees, and high transaction volumes. 

That’s where Link My Books comes in, it automates the import of transactions, handles taxes accurately, and simplifies reconciliation. 

Plus, it offers advanced reporting on key metrics like sales trends and profitability, making it a must-have for Amazon sellers who want to streamline and optimize their financial management. This combo makes for a powerful Amazon bookeeping software option for sellers.

Top Features of Quickbooks

• Simplified Self-Assessment: QuickBooks makes the often complicated process of preparing self-assessment tax returns much easier. This is a huge plus for small business owners and sole traders who handle their own finances.
• HMRC Compliance: The software is fully compliant with HMRC regulations and even includes a VAT error checker. This feature is essential for UK-based Amazon sellers, to ensure your VAT returns are accurate and in line with tax laws.
• Cash Flow Monitoring: QuickBooks gives you a clear view of your business’s cash flow, making it easier to track, manage, and understand your finances. This helps you make smarter decisions about where to spend, save, or invest.
• Sales Forecasting: With QuickBooks, you can create detailed sales forecasts. These reports help you anticipate future trends, plan for seasonal changes, and set realistic business goals.
• Customizable Class Tracking: QuickBooks lets you categorize and track your income and expenses by different segments of your business, like marketplaces or sales channels. When you integrate it with Link My Books, it automatically assigns sales, fees, and other transactions to the right class, making your Profit & Loss (P&L) statements even more accurate and insightful.

Ease-of-Use and Customer Support

QuickBooks is designed for users with some basic accounting knowledge. The software comes with a learning curve so be prepared for that.

Educational Resources:

• The QuickBooks website is packed with helpful resources to guide you through its features. You’ll find tutorials, guides, and a regularly updated blog covering important topics like inventory management and sales tax.

Customer Support:

• Depending on your plan, QuickBooks offers phone and chat support for personalized help. There’s also the QuickBooks community forum, where you can ask questions, share advice, and learn from other users.

Quickbooks Pricing

For UK Customers

*The image reflects a current offer 

Simple Start is best for freelancers and very small businesses with minimal accounting needs. Essentials suits small businesses that require basic features plus bill management and time tracking. Plus is ideal for businesses that need to manage inventory and track project profitability.

Advanced is designed for larger businesses that need advanced reporting, more users, and premium support.

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For US Customers

*The image is reflecting a current discount

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For AU Customers 

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If you subscribe now you can get live expert assistance free for 30 days*

You can try QuickBooks Amazon Integration for 14 days free of charge. 

• No credit card is required
• Easy 15-minute setup

Zoho Free Accounting Software for Amazon Sellers

Zoho Books is a cost-effective solution for Amazon sellers, particularly those who are just starting out or have a tight budget. 

While free tools like Zoho Books offer some useful features they come with significant limitations.

Using Zoho Books means you'll need to manually download data from Amazon, separate revenue by country and tax rate, and categorize expenses by tax rate. Manually handling these tasks is complex and prone to errors, which could ultimately cost you more than investing in a solution like Xero and Link My Books.

With Xero and Link My Books, you can be 100% confident that your accounting is accurate, saving you time, stress, and potential financial errors.

Top Features of Zoho Books

• User-Friendly Interface: Zoho Books is designed to be simple and straightforward, making it easy for beginners to navigate and manage their accounts without needing deep accounting knowledge.
• Customizable Invoices: You can create and send professional-looking invoices with Zoho Books, customizing them to match your brand. This feature is perfect for sellers who want to maintain a consistent image across all their communications.

Limitations:

• Restricted Features: The free plan caps the number of invoices at 1,000 per month and lacks advanced tax tools. As your business grows, you may need to upgrade to a paid plan to access more comprehensive features.
• Limited Integrations: While Zoho Books integrates with some eCommerce platforms, it doesn’t offer the same level of connectivity as QuickBooks or Xero.

Zoho Pricing

For UK Customers

The Free Plan is for businesses with minimal accounting needs. Paid plans start at £12/month, offering additional features and higher limits.

For US Customers

For AU Customers 

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Wave for Amazon Sellers

Wave is a free accounting software option that offers essential invoicing and accounting features, it’s a suitable choice for sellers who need basic functionality. 

However, it also has limitations, particularly for Amazon FBA sellers. With Wave, you’ll need to manually download data from Amazon, then separate revenue by country and tax rate, as well as expenses by tax rate, before accounting for those figures yourself. This manual process is complex and can easily lead to errors, which can potentially cost you more in the long run. 

Investing in a solution like Xero with Link My Books will make sure your accounting is accurate and efficient, giving you peace of mind that your financials are correct.

Top Features of Wave

• Free Accounting and Invoicing: Wave’s free plan gives you a full set of tools for tracking income and expenses, sending invoices, and managing receipts. It’s for sellers who want to keep costs low while staying on top of their finances.
• Customizable Invoices: Just like with Zoho, Wave lets you create and send invoices that can be customized to fit your brand. It also includes automated payment reminders, helping you get paid on time and keep your cash flow steady.
• Collaboration Tools: Wave makes it simple to add partners or accountants to your account, allowing multiple users to work together on managing your finances. This is especially helpful for small teams or family-run businesses.

Limitations:

• No Amazon FBA Integration: A major downside of Wave is that it doesn’t integrate directly with Amazon FBA. This means you’ll have to manually enter and reconcile your Amazon transactions, which can take a lot of time.
• Limited Advanced Features: While Wave covers the basics well, it lacks the more advanced tax tools and integrations that other accounting software options offer.

Wave Pricing

New Wave account sign-ups are limited to US and Canadian business owners only. Wawe doesn’t provide support for this product outside of this region.

• Free Plan: Wave offers free accounting services, including invoicing, billing, and expense tracking. Payroll is not included in the free plan.
• Payroll Add-On: Available as a paid service, where the pricing varies depending on the state. In tax-service states, Wave handles payroll taxes on your behalf, whereas in self-service states, you manage payroll taxes manually.

For US Customers

*The pricing on the image is for the US market.

Wave’s basic accounting and invoicing tools are free, making it a good choice if you’re a budget-conscious seller. If you need more advanced features, you can upgrade to a monthly plan for $16/month, which is around £12/month.

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Sage for Amazon Sellers

Sage is a well-known player in the accounting software world, especially for more established Amazon sellers. It’s packed with features like inventory management and financial reporting, making it a great fit for sellers with more complex needs.

However, while Sage does integrate with third party vendors, this setup tends to be pricier and trickier to get right compared to using Xero with Link My Books. Xero and Link My Books offer a more cost-effective and user-friendly solution, making it easier to manage your Amazon business finances accurately and efficiently.

Top Features of Sage

• Inventory Management: Sage offers detailed inventory tracking, including automatic updates on stock levels and low-stock alerts. This is crucial for Amazon sellers who need to stay on top of their inventory to avoid running out of stock or overordering.
• Comprehensive Reporting: Sage stands out with its financial reporting capabilities, providing deep insights into your business’s performance. Whether it’s cash flow forecasts or profitability analysis, Sage gives you the data you need to make smart business decisions.
• Third-Party Integrations: Although Sage doesn’t directly integrate with Amazon, it can connect to eCommerce platforms through third-party vendors. This lets you manage your entire sales process within the Sage environment.

Sage Pricing

For UK Customers 

The Basic Package starts at £15/month, with additional features available on higher-tier plans.

For US Customers 

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How to choose the best Amazon Accounting Software for you 

When choosing the right Amazon accounting software for your business, there are several key factors to consider. It’s important to balance cost with the features and support you need to manage your finances effectively. While free software can be tempting, make sure you consider the possible drawbacks. Here are the things to look for:

Accuracy

Mistakes with Amazon’s fees and taxes can be expensive. Look for software that ensures precise tracking, tax calculation, and financial reporting. 

Link My Books guarantees accuracy by automating the import of Amazon sales data, eliminating the risk of human error.

Time-Saving Ability

Your accounting software should simplify tasks like invoicing, reconciliation, and tax calculations to save you time. Link My Books integrates with Xero and QuickBooks, automating these processes so you can focus on growing your business.

Useful eCommerce Insights

Beyond basic accounting, your software should offer insights specific to eCommerce, helping you understand how your business is performing in the market. Link My Books provides built-in financial analytics and benchmarking, giving you the information you need to make strategic decisions.

Ease of Use

The software should be easy to use, especially if you’re new to accounting. While feature-rich options may be appealing, consider if you really need all the extras or if a simpler solution would be more effective. Make sure the software is easy to navigate and doesn’t have a steep learning curve.

Customer Support

If you run into technical issues or need help, quick and effective support can keep your business running smoothly. Look for software that offers support through live chat, email, and phone, so you can get help in the way that suits you best.

Value for Money

Cost is always a factor, especially for small businesses. While free software might save money upfront, it often has limitations that could end up costing more in the long run due to errors or lack of features. Consider the value of paying for software like Xero with Link My Books, which offers comprehensive features and accuracy.

eCommerce-Specific Features

Your accounting software should have features tailored to Amazon businesses, like inventory tracking, Amazon integration, and sales tax calculation. As your business grows, having these features will become even more important.

Additional Considerations:

• Accounting Features: List the features you need, dividing them into "essential," "good to have," and "not necessary." Even if you’re just starting, features like inventory tracking and cash flow reporting will become more valuable as you scale.
• Free Trials: Take advantage of free trials to test the software before you commit. This is a great way to see if the software meets your needs and is easy to use.

How do Our Recommended Software Compare?

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Why accounting software alone is not enough

Accounting software is essential for keeping accurate financial records, but accounting software alone is not enough for e-commerce businesses. Amazon accounting automation tools make financial management a lot easier by automating tasks like tax calculation, payout reconciliation, and cost of goods sold tracking. This is especially helpful for sellers using Fulfilled by Amazon (FBA), where Amazon handles storage and shipping, adding extra costs and complexities to manage.

Whether you’re using FBA or handling logistics on your own, accounting software is key for keeping track of your finances, generating reports, and managing inventory accurately. While you could get by without it, this software significantly lightens the load, making it an essential tool for efficiently managing your Amazon business.

Why Amazon Sellers Choose Link My Books?

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Link My Books automates bookkeeping for eCommerce businesses, especially Amazon sellers. What makes Link My Books stand out is how it tackles the specific challenges that Amazon FBA sellers face.

Top Features of Link My Books

Let's jump into it with Link My Books' top features.

Automated Payout Reconciliation

Link My Books automatically matches your Amazon sales, refunds, fees, and taxes with your accounting software, giving you clear and accurate financial data. 

It supports all Amazon marketplaces and integrates with other platforms like eBay, Etsy, and Shopify, so you can manage your entire eCommerce business from one place.

Accurate Tax Calculation 

Managing taxes across different regions with varying tax laws is a major challenge for Amazon sellers. In fact, 75% of our Amazon sellers discovered they were overpaying taxes before using Link My Books. Our software calculates the correct VAT or sales tax on every sale, ensuring accuracy based on each jurisdiction.

Cost of Goods Sold (COGS) Tracking

Tracking your Cost of Goods Sold on Amazon (COGS) is vital for understanding your profit margins. Link My Books ensures that COGS is accurately recorded, helping you get a clear picture of your true costs and how they impact your bottom line. By keeping a close eye on COGS, you can make smarter pricing decisions and improve your overall profitability.

Real-Time Reporting and Analytics

Link My Books gives you access to real-time financial reports and analytics, tailored for eCommerce businesses. You'll get insights into your profitability, sales performance, Amazon account level reserve, and cash flow, helping you make informed decisions.

Benchmarking

Gain industry insights from anonymous data on key metrics like sales growth, refund ratios, and fee ratios. Link My Books focuses on percentage changes and trends rather than exact numbers, helping you see if your business is following broader market trends or experiencing unique changes.

User-Friendly Setup and Interface

Link My Books is designed to be easy to use, even if you're new to  bookkeeping for Amazon sellers. Setup is quick, with most users up and running in just 15 minutes. If you need help, we offer a free onboarding call with our team of experts, or you can explore our blog posts, webinars, guides, and videos for additional support.

Link My Books Pricing

We've kept our pricing as straightforward as possible. Try our new interactive pricing chart for accurate expense calculation:

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Our Lite plans start from just £13/month or $17/month if you’re in the US, they include:

• Connect 1 sales channel
• 3 months of historical data

Our Pro plans start from just £23/month or $29/month if you’re in the US, they include:

• Connect up to 5 sales channels
• 12 months of historical data

Larger plans are available too with more orders and more channels.

All Link My Books yearly members can get a free two months of our software. And, Amazon sellers can add as many users as they like to all plans.

Get started with Link My Books for Amazon sellers for free today.

How Link My Books Saves You Time and Money

• Reduce Bookkeeping Time: Most users save hours each month with Link My Books' automated processes that handle data entry and reconciliation. This means you can spend more time growing your business instead of managing the books.
• Prevent Overpayment of Taxes: With accurate tax calculations, Link My Books helps prevent the common problem of overpaying VAT or sales tax, saving your business money over time.
• Scalable Pricing Plans: Whether you’re just starting out or running a larger operation, Link My Books offers flexible pricing plans that grow with your business.
• Designed for Amazon Sellers: Link My Books is tailored specifically for Amazon sellers and eCommerce businesses, making it ideal even for those with no accounting experience. It automatically breaks down all your sales, refunds, fees, and taxes, posting summaries directly into your Xero or QuickBooks accounts.

Which Amazon Accounting Software is Best for You?

Navigating bookkeeping for Amazon sellers can be frustrating, but the right accounting software can simplify the process significantly. For tasks like tracking sales tax, managing inventory, preparing taxes, and forecasting sales, accounting software saves you both time and money.

When choosing the best accounting software for your needs, you should prioritize how easily it integrates with your Amazon account, the types of reports it offers, and the quality of customer support. This is where the powerful combination of Xero or QuickBooks Online with Link My Books comes into play.

You can get started with Link My Books' software for Amazon sellers for free today. Sign up and book an onboarding call to talk through your options.