5 Best Ebay Accounting Software in 2025: Save Time by Automating your eBay Bookkeeping!

One of the key principles of running your business is knowing your numbers. But bookkeeping can become overwhelming as soon as you start to scale.

Between managing sales, tracking expenses, and staying on top of taxes, it’s easy to feel buried in numbers. 

The right eBay accounting software can take the stress out of managing your finances, giving you back the time and energy to focus on growing your business. 

To take it a step further you can automate everything with Link My Books and never have to worry about manual input again.

In this article, we'll break down the best accounting software options to help you streamline your bookkeeping. We’ll go through features and give you a comparison table so you can easily choose what’s best for you. 

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Top Accounting Software for eBay Sellers

1. Xero with Link My Books
2. QuickBooks Online with Link My Books
3. Wave
4. Sage
5. Freshbooks

Xero: Best Overall

Xero is an excellent eBay accounting software that offers a set of features designed to simplify your financial management. To integrate Xero directly with eBay, you can use Link My Books. It will consolidate your transactions, eBay fees, shipping and supplier data and sync that information directly to your Xero account.

Xero Key Features

• Syncs with Over 1,000 Third-Party Apps: This means you can easily link it to other tools you already use, like CRM systems, payroll software, inventory management or cash flow forecasting apps.
• Inventory Tracking and Sales Tax Management: Xero’s inventory tracking keeps an eye on your stock levels in real-time, so you know when it’s time to reorder. Plus, it helps you manage sales tax by automatically calculating the right rates based on where you’re selling. This is especially handy if you’re selling in different regions.
• Accepts Online Payments: Xero integrates with all the popular payment options like Stripe, Apple Pay, and Google Pay. You can add a “Pay Now” button to your invoices. Plus, Xero automatically matches payments to invoices, so your accounts are always in order, and you don’t have to worry about mistakes in your cash flow.
• User-Friendly Dashboard: The dashboard is intuitive, showing you everything you need to know at a glance, cash flow, outstanding invoices, and upcoming bills.

Why Link My Books & Xero combine so well for eBay accounting

Xero handles your day-to-day accounting needs, but as an eBay seller, you’re dealing with a lot of transactions, sales, refunds, fees, and taxes. Which can be a hassle to manage manually. The best way to overcome this is to integrate your eBay bookkeeping software.

That’s where Link My Books comes in. It automates the import of all your eBay transactions directly into Xero, categorizing them accurately, so your books are always up to date without lifting a finger. 

What other eBay sellers say about Link My Books

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Link My Books+Xero eBay integration is easy to set up. It only takes a couple of steps. 

How Xero+Link My Books Automates Your eBay Bookkeeping

Here’s a quick overview of how Link My Books Works with Xero.

1. Connect eBay and Xero to Link My Books:

The first step to automating your eBay bookkeeping is to connect your eBay seller account and Xero to Link My Books. This integration is straightforward and will help you streamline everything. 

Once connected, Link My Books will automatically sync with your eBay account and pull in all the financial data from your sales, refunds, and fees.

2. Automated Transaction Validation with Each Payout:

2. Every time you receive a payout from eBay, Link My Books validates each transaction that contributes to that payout. Whether it’s a simple sale, a refund, or a fee, Link My Books verifies the specifics, like the buyer’s location and applicable tax rules, to make sure everything is handled correctly.

3. Generate a Detailed Summary Invoice in Xero:

After validating the transactions, Link My Books generates a clean summary invoice in Xero. This invoice breaks down the entire payout, clearly categorizing each component into sales, refunds, and fees. This process makes sure that your financial records are accurate and compliant with tax regulations.

4. Effortless Reconciliation with One-Click Matching:

The real beauty of this system is in the reconciliation. The summary entry created by Link My Books in Xero is designed to match the actual deposit you receive in your bank account down to the last penny. With just one click, you can reconcile the entry in Xero, confirming that everything lines up perfectly. 

Link My Books+Xero eBay integration is easy to set up, takes only 15 minutes, and doesn’t require a credit card.

Xero Pricing

For UK Customers

While Xero’s Ignite plan is budget-friendly, it does come with some limitations, like only allowing 20 invoices and 10 bills per month. If your business is growing, you might want to upgrade to Grow, which offers more flexibility. And if you deal with multiple currencies, the Comprehensive plan has you covered.

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For US Customers

For AU Customers 

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Try the Link My Books+Xero eBay integration  for free for 14 days, it’s free. You don’t need a credit card and it takes 15 min to set up. 

QuickBooks Online: Most User-Friendly

QuickBooks Online is another go-to option for eBay accounting software, known for its ease of use and features. It’s designed to make accounting as simple as possible, even for those without a background in finance. 

While it does integrate with eBay via the Connector by QuickBooks, this integration is often faulty and it doesn’t transfer data correctly. 

But, when you add Link My Books to the mix, it will actually help you automate your accounting without any errors. 

QuickBooks Key Features

• Mobile App for On-the-Go Management: QuickBooks’ mobile app is robust, allowing you to manage your finances, send invoices, and track expenses from anywhere. This is especially handy for eBay sellers who need to stay on top of their business while on the move.
• Sales Tax Tracking & Quarterly Tax Estimation: QuickBooks takes the stress out of tax season by tracking your sales tax and estimating your quarterly taxes, ensuring you’re always prepared.
• Freelancer-Friendly: QuickBooks is ideal for freelancers and those with multiple income streams, as it simplifies the process of tracking income and expenses from various sources, making tax filing easy.

Why Link My Books & QuickBooks combine so well for eBay accounting

Link My Books automatically syncs your eBay transactions with QuickBooks, categorizing everything from sales and refunds to fees and taxes. This automation not only saves you time but also reduces the risk of errors, so you can be confident that your books are always accurate.

How QuickBooks+Link My Books Automates Your eBay Bookkeeping

It only takes a few simple steps to automate everything. Here’s what to do to integrate QuickBooks with Link My Books:

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1. Connect eBay and QuickBooks to Link My Books:
   Start by linking your eBay account and QuickBooks to Link My Books. This connection ensures that your financial data flows seamlessly between platforms.

2. Automated Transaction Validation:

Every time you receive a payout from eBay, Link My Books reviews each transaction within that payout. It checks every order's details to ensure the correct tax treatment is applied, leaving no room for errors.

3. Generate a Clean Summary in QuickBooks:

Link My Books then creates a clear summary in QuickBooks via a journal entry. This summary breaks down the payout into sales, refunds, and fees, assigning them to the appropriate accounts while applying the correct tax rates.

4. Effortless Reconciliation:

The entry in QuickBooks is designed to match your bank deposit exactly. With just one click, you can reconcile the entry, ensuring that your records are accurate and up-to-date.

QuickBooks Pricing

For UK Customers

*The image reflects a current offer of 3 months free

The entry-level plan of QuickBooks doesn’t include inventory management, which could be a drawback if you’re managing a lot of products. If inventory tracking is crucial for your eBay business, you’ll need to upgrade to QuickBooks Online Plus.

For US Customers

* The image reflects a current discount 

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For AU Customers 

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

You can try our QuickBooks eBay integration for 14 days free of charge. 

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

Wave: Top Free Accounting Software

Wave offers free accounting and invoicing tools that cover the basics, making it perfect for small eBay sellers or those just starting. It’s simple to use, yet powerful enough to help you manage your finances effectively. If you’re looking for a free eBay bookkeeping software, Wawe is a good choice. 

Wave Key Features

• Customizable Sales Tax Tracking: Even though it’s free, Wave offers customizable sales tax tracking, helping you stay compliant without spending a dime.
• Multi-Business Management: Have more than one business? No problem. Wave lets you manage multiple businesses from one account, all for free.
• Basic Cash Flow Tracking: Wave provides simple cash flow tracking, giving you a clear picture of your business’s financial health at any time.

Wave is fantastic for basic accounting needs, but it does have its limitations. It lacks built-in inventory management and doesn’t integrate with as many e-commerce inventory apps such as Xero or QuickBooks. This means you’ll need to manually enter more data, or connect to Zappier and choose which data to import. 

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

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 that’s around $12/month. 

Sage Business Cloud Accounting: Best for Scalable Financial Management

Sage Business Cloud Accounting is a great option for eBay sellers who need a scalable solution. As your business grows, Sage grows with you, offering more advanced features that can handle increasing complexities in your financial management. It’s especially strong in financial reporting, giving you detailed insights that can help guide your business decisions.

Sage Key Features

• Cloud-Based Accounting: Sage’s cloud-based platform allows you to manage your finances from anywhere, providing real-time access to your data.
• Detailed Financial Reporting: Sage excels in reporting, offering a wide range of reports that give you a deep dive into your business’s financial performance.
• Bank Integration and Reconciliation: Sage makes it easy to connect your bank accounts and reconcile your transactions, ensuring your records are always accurate.

Sage is powerful, but it might not be the best fit for all eBay sellers. It lacks the robust inventory management features found in Xero and QuickBooks, which could be a deal-breaker if you have a lot of products to manage. 

While it does integrate with third-party platforms it might end up being a more costly solution. 

Sage Pricing

For UK Customers 

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

For US Customers 

*The prices stated are for one user 

FreshBooks: Best for Invoicing

FreshBooks is well-known for its invoicing capabilities, making it a top choice for eBay sellers who want to maintain a professional image while keeping their finances in order. It’s user-friendly and offers a range of features designed to simplify the invoicing process, from automation to customization.

FreshBooks Key Features

• Invoice Automation: FreshBooks can automatically generate recurring invoices, saving you time and ensuring your customers are billed on schedule.
• Sales Tax Tracking: Like the other options, FreshBooks tracks sales tax, helping you stay compliant with tax laws.
• Freelancer Features: FreshBooks offers tools similar to QuickBooks, like tracking sales taxes and profits, making it easier to manage your finances as a freelancer or small business owner.

FreshBooks is excellent for invoicing, but it falls short in other areas, like inventory management. If you need more comprehensive features without spending more, Xero or Zoho might be better suited to your needs. Additionally, FreshBooks doesn’t integrate with some popular eBay apps, which could limit its functionality for your business.

FreshBooks Pricing

For UK Customers

FreshBooks offers four plans. Lite for freelancers with up to 5 clients, Plus for growing businesses with up to 50 clients, Premium for unlimited clients, and Select, a custom-priced option with advanced features and a dedicated account manager. Each plan includes essential tools like invoicing, expense tracking, and accounting.

For US Customers

For AU Customers

What to Look for in eBay Accounting Software

When choosing accounting software for your eBay business, it’s important to find a solution that fits your unique needs. Here’s what to keep in mind:

Accuracy

Accurate bookkeeping is a must. The software should keep your finances precise, reducing the chance of errors in your transactions, tax calculations, and reports.

Time-Saving Features

Look for automation features that can save you time, like automatic transaction imports and reconciliation. This frees you up to focus on growing your business rather than getting stuck in the details.

E-commerce-Specific Features

Choose software that offers insights tailored to e-commerce, such as financial analytics and industry benchmarks. These can help you make smarter, data-driven decisions.

Affordability

You want software that fits your budget but still gives you the features you need. Don’t just go for the cheapest option—think about what you’re getting for your money, including must-have features and good customer support.

Ease of Use

The software should be simple and easy to navigate. You don’t want to spend hours figuring out how to use it. Look for something with a clean, intuitive interface that makes managing your finances straightforward.

Setup Process

Getting started should be quick and painless. The software should let you connect your eBay account easily, with guides or a setup wizard to help you get up and running without any headaches.

Integrations

Make sure the software can integrate with other platforms and services you use, like other e-commerce sites, payment processors, and shipping tools. The more it can connect, the more streamlined your operations will be.

Customer Support

Good customer support is essential. The software provider should offer multiple ways to get help and respond quickly when you have questions or run into issues.

Our Recommendation

Choosing the right accounting software for your eBay business comes down to your specific needs and preferences. 

Think about factors like inventory management, eBay VAT calculations, eBay sales reports, third-party integrations, pricing, and any special features that align with your business.

Not sure what you need? Read more about the best eBay tools for sellers.

We highly recommend looking into Xero or QuickBooks Online. When combined with Link My Books, these platforms offer a powerful solution for eBay sellers, automating your bookkeeping so you can focus more on growing your business.

Here’s a comparison table so you can see how they stack up at a glance.

eBay Sellers Deserve Accurate, Automated Books

Are you ready to take your bookkeeping to the next level? Discover the benefits of Link My Books and watch your accounting process evolve seamlessly.

No more stress, sign up for our free trial and start your journey towards worry-free financial management. Click the button below to explore more.

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You’ll find everything you need to get started on our website, or keep reading for more details. Automate your bookkeeping with Link My Books and watch your business soar to new heights! 

Why Accounting Software Alone is Not Enough

Managing finances as an eBay seller involves unique challenges that standard accounting software might not fully address. Here’s why:

• Complex Fee Structures: eBay’s various fees like, listing fees, final value fees, and promotional fees, can be complex to track accurately. 
• Multiple Sales Channels: Many eBay sellers operate on multiple platforms, making it challenging to consolidate financial data and inventory tracking across all channels with just standard accounting software.
• Varying Tax Regulations: eBay sellers often ship to different regions, each with its own tax laws. Standard accounting software may not be equipped to handle varying sales tax rates and VAT requirements accurately.
• Reconciliation of Payouts: eBay payouts can include multiple transactions, refunds, and fees in a single deposit, making it difficult to reconcile these amounts accurately without specialized tools.
• Inventory Management: Keeping track of inventory across multiple sales channels, including eBay, can be overwhelming. Basic accounting software may not provide the advanced inventory tracking needed for a growing e-commerce business.
• Detailed Reporting Needs: eBay sellers often need detailed insights into sales trends, profitability, and performance metrics, which may require more advanced reporting capabilities than standard accounting software offers.

Link My Books saves you time by automating your tasks. The platform verifies each order and refund, checks the destination country, and ensures precise tax calculations. It groups sales by destination country, simplifying tax and VAT accounting based on each country’s rules, ensuring accurate tax returns every time.

Why Link My Books Makes eBay Accounting Simple

Link My Books is all about making eBay accounting easier. With features like financial analytics, benchmarking, and automated payout reconciliation, you get clear insights into your business's performance. Plus, the setup is quick and easy, with a wizard that guides you through connecting your eBay account and configuring your tax rates.

Automated Payout Reconciliation

Link My Books automatically reconciles your Amazon sales, refunds, fees, and taxes with your accounting software, giving you full visibility and unbeatable accuracy. The software supports all Amazon marketplaces and integrates with platforms like eBay, Etsy, and Shopify.

Accurate Tax Calculation

Managing taxes can be tricky, especially when selling across different regions with varying tax laws. Link My Books calculates the tax on every sale, ensuring the correct VAT or sales tax is applied based on the jurisdiction.

Real-Time Reporting and Analytics

With Link My Books, you gain access to real-time financial reports and analytics tailored to eCommerce businesses. These reports offer insights into your profitability, sales performance, and cash flow.

Benchmarking

Get industry insights from anonymized data on key metrics like sales growth, refund ratios, and fee ratios. This helps you understand whether your business's performance aligns with broader market trends or if it's experiencing unique change.

5 Easy Steps to Get Started with Link My Books

Our setup wizard is intuitive and easy to use, guiding you through each stage, from selecting the accounts in Xero or QuickBooks to configuring your tax rates. Here’s how it works:

Step 1: Register for Link My Books and Connect Your eBay Seller Account

Sign up for Link My Books and connect your eBay account. Our platform is compatible with all major sales channels, making it easy to start automating your bookkeeping.

Step 2: Connect Your Accounting Software

Next, link your accounting software (Xero or QuickBooks) to your Link My Books account. This integration ensures that your sales, refunds, fees, and taxes are accurately accounted for.

Step 3: Configure Your Tax Rates and Accounts

Set up your tax rates and accounts using our intuitive setup wizard. You can either accept the default tax rates provided by Link My Books or establish your own rates.

Step 4: Begin Automating Your eBay Business Accounting

Once configured, Link My Books will automatically fetch all necessary data to account for your sales, refunds, fees, and taxes. The platform verifies each order and refund, ensuring precision and eliminating manual entry.

Step 5: Review Your Bookkeeping Reports

After each payout, Link My Books generates a summary invoice that breaks down your sales, refunds, fees, and taxes. You can review these reports in Xero or QuickBooks, where they’re neatly displayed in your profit and loss statements.

The Best Accounting Software Solution for eBay Sellers?

If you’re an eBay seller looking to streamline your financial management, investing in accounting software like Xero or QuickBooks Online, especially when integrated with Link My Books, is a smart move. This powerful combo automates your bookkeeping tasks, saving you time and reducing errors so you can focus on growing your business.

With options like Wave, FreshBooks, and Sage, you can find a solution tailored to your unique needs, whether you need inventory management, invoicing, or a user-friendly interface. But for a cost-effective and top-quality accounting solution, pairing Xero or QuickBooks with Link My Books is hard to beat.

Redefine your accounting experience with Link My Books! 

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Don’t miss out on optimizing your financial management with our free trial. Let us handle the numbers, so you can focus on scaling. 

Frequently Asked Questions

1. What is the best accounting software for eBay sellers?

The best accounting software for eBay sellers depends on your specific needs. However, Xero and QuickBooks Online are often top choices because they offer comprehensive features, ease of use, and seamless integration with platforms like Link My Books, which automates much of the bookkeeping process.

2. How do I manage taxes as an eBay seller?

Managing taxes as an eBay seller involves tracking sales tax for different jurisdictions and accurately reporting income to avoid penalties. Accounting software like Xero and QuickBooks can automate tax calculations and filings, while tools like Link My Books can automatically import and categorize transactions, making tax management easier and more accurate.

3. Can I use free accounting software for my eBay business?

Yes, free accounting software like Wave can be used for basic bookkeeping tasks, such as invoicing and expense tracking. However, it may lack advanced features like inventory management or detailed tax reporting, which are essential as your business grows.

4. How do I keep track of eBay sales for tax purposes?

To keep track of eBay sales for tax purposes, it's important to use accounting software that integrates with eBay. This software should be able to automatically import sales data, categorize transactions, and generate reports for tax filings. Link My Books, when paired with Xero or QuickBooks, is particularly effective for this purpose.

5. Do I need an accountant if I use accounting software?

While accounting software can handle many of the day-to-day tasks, an accountant can provide valuable insights, help with tax planning, and ensure that your business complies with all tax regulations. Many eBay sellers use a combination of software for regular tasks and consult an accountant for more complex financial issues.

6. How do I reconcile my eBay transactions?

Reconciling eBay transactions involves matching your sales and fees from eBay with the deposits in your bank account. Accounting software like Xero or QuickBooks can help automate this process, especially when integrated with Link My Books, which automatically pulls in your eBay data and matches it to your bank transactions.

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Be sure to sign up for our free trial, see what Link My Books can do for you, try now and experience the power of automated bookkeeping so you can make a decision that's best for you, with all the information you need!

“It saves me time, money and the stress of making sure everything is correctly posted in Xero. I can’t explain how satisfying Link My Books is.“

Neil N, Amazon, eBay & Etsy Seller
Verified, Xero App Store

“Saves us a lot of time and confusion. We are an e-commerce multi channel retailer and being able to confidently prepare our tax returns is a big advantage.“

Malcolm M, Amazon, eBay & Shopify Seller
Verified, QuickBooks App Store

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Be sure to sign up for our free trial, see what Link My Books can do for you, try now and experience the power of automated bookkeeping so you can make a decision that's best for you, with all the information you need!

Disclaimer: Data is accurate as of September 2024. Prices may fluctuate depending on your region and providers can change prices. The prices shown and links provided in the article are for users based in the UK.

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Additional Resources: 

- Understanding eBay Fees: A Comprehensive Guide

- How to Connect eBay to Xero: A Step-by-Step Tutorial

- Which eBay Reports to Use for eBay Seller Bookkeeping

- eBay Seller Accounting Spreadsheet: Free Download

- Ecommerce Accounting: What You Need to Know