Top 6 eBay Accounting Software in 2025

Managing finances as an eBay seller can be stressful, especially with the complexity of tracking sales, and inventory. Moreover, the business involves more than listing products and processing orders. As sales grow, managing finances becomes complex. Tracking fees, reconciling payments, calculating taxes, and forecasting cash flow can overwhelm even seasoned sellers. 

That’s where eBay accounting software comes in. The right software automates accounting tasks, reduces errors, and provides actionable insights. But with countless options available, how do you choose?

We’ll help you with that. In this article, we discuss some of these options. We also highlight how pairing platforms like QuickBooks or NetSuite with Webgility helps you eliminate manual reconciliation, maintain accurate inventory, and automate purchase orders.

7 key features to consider when choosing the accounting software for eBay sellers

When choosing accounting software for eBay sellers, it’s essential to focus on features that streamline financial management, ensure compliance, and provide actionable insights. Here are some key features to consider:

Expense tracking and reporting

Your accounting software should track all your expenses, including shipping costs, eBay seller fees, PayPal charges, and other operational expenses. With advanced reporting tools, you can easily monitor your profitability and make informed, data-driven decisions.

Integrations

Seamless integration with eBay is non-negotiable. The software should automatically sync sales, fees, refunds, and shipping costs to eliminate manual data entry. Multi-channel sellers should prioritize platforms that also connect to Amazon, Shopify, and Walmart. Webgility, for instance, acts as a bridge between eBay and accounting systems like QuickBooks, eliminating manual data entry.

Periodic or real-time syncing

Accurate financial reporting relies on aligning transactions with accounting periods (monthly, quarterly, or annually). Look for software that automatically syncs data in real time, ensuring your books are always audit-ready. Delayed syncing can lead to mismatched records and compliance risks.

Inventory management

Choose software that offers real-time inventory sync between eBay and your accounting software. Products like Webgility, when connected to QuickBooks and Netsuite, can help you maintain an up-to-date inventory, track stock levels, update product listings and pricing, and calculate COGS and sales per channel. You can prevent overselling and overstocking by keeping accurate tabs on your inventory.

Tax compliance and automation

Depending on where you’re located, the right software should handle tax calculations for different regions, including VAT, GST, or sales tax. It should also assist with tax filing and generate reports to ensure compliance with tax authorities.

Multi-currency support

The software should facilitate accounting for multiple currencies based on real-time exchange rates to help you sell and expand internationally. The software should be able to provide accurate financial reports for your global transactions.

User-friendly dashboard and automation

An intuitive dashboard with automation features like invoice generation, recurring billing, and payment reminders can save you time and simplify your accounting. Automating these repetitive tasks will ensure accuracy and efficiency.

Best eBay accounting software in 2025

Running an eBay ecommerce store requires integrating it with accounting solutions. Here are the best solutions.

1. QuickBooks + Webgility

QuickBooks is one of the most popular accounting solutions. It can help you with bookkeeping, invoicing, expense tracking, inventory management, etc. QuickBooks is one of the most widely used solutions for small to medium-sized businesses. It offers both online and desktop versions that cater to different types of business needs.

This solution is ideal for eBay sellers who want a simple yet powerful accounting tool with integrated inventory management and detailed financial reporting..

Why integrate with Webgility?

Connecting eBay and QuickBooks with Webgility helps you sync sales orders to Quickbooks in real-time. Webgility also keeps your inventory data up-to-date via real-time syncing of orders to QuickBooks Inventory. This combination automates your accounting by directly syncing your eBay orders, inventory, and expenses with QuickBooks. Eliminating manual data entry, it saves you time and reduces errors.

Key features of QuickBooks

• Invoicing and payment processing: The service lets eBay sellers create professional invoices for their transactions and accept payments via credit card or bank transfer.
  
  
• Sales tax calculation: The Sales Tax Center in Quickbooks lets you add and edit tax agencies, rates, and settings.
  
  
• Financial reporting: QuickBooks offers various financial reports that give sellers insights into their profits, expenses, and overall business performance. These reports can help sellers make informed decisions.

Benefits of integrating Webgility with QuickBooks 

Integrating Webgility with QuickBooks offers several benefits for eBay sellers, particularly in simplifying and automating essential business processes. Here’s how this integration can add value:

• Real-time data syncing: QuickBooks typically updates data periodically, leaving room for delays. Webgility, on the other hand, enables near real-time syncing of orders, inventory, and pricing. It thus keeps your accounting data accurate and up to date. This is an especially useful feature during high sales volumes.
  
  
• Comprehensive multi-channel integration: QuickBooks integrates with select ecommerce platforms. Connecting Webgility increases the integration base to cover channels such as Amazon, eBay, Shopify, Etsy, and more. This ensures seamless data flow from all sales platforms into QuickBooks, centralizing operations.
  
  
• Advanced inventory management: QuickBooks’ inventory tracking is limited, particularly for businesses operating on multiple platforms. Webgility synchronizes inventory levels across all sales channels and QuickBooks. It thus prevents stockouts, overselling, and inaccuracies while providing detailed inventory reports and alerts.
  
  
• Enhanced financial reporting: QuickBooks reports lack ecommerce-specific insights. Webgility bridges this gap by offering tailored analytics, including channel-specific performance, sales trends, and profitability. These insights empower businesses to identify their most successful platforms and optimize their strategies.
  
  
• Simplified sales tax compliance: Managing multi-state sales tax with QuickBooks alone can be cumbersome and error-prone. Webgility simplifies filing sales taxes by ensuring accurate financial data is synced in real time. It thus ensures compliance with the latest tax rules and simplifies the reporting process for businesses operating across multiple jurisdictions.

Case Study: How Channie’s used Webgility to connect QuickBooks to eBay and Deliver Growth

Pros:

• Keeps your financial and sales data up-to-date with real-time synchronization
• Supports invoicing, expense tracking, payroll management, tax preparation, inventory tracking, and more
• QuickBooks integrates with numerous third-party apps and tools, including ecommerce platforms, CRM systems, and payment processors

Cons:

• Some plans have limitations on the number of users

Pricing

QuickBooks Online has a four-tier pricing:

• Simple Start: $17. 50/month
• Essential 32.50/month 
• Plus: $49.50/month
• Advanced: $117.50/month

For their updated pricing plans, check their pricing page.

2. NetSuite integrated with Webgility

NetSuite accounting software makes tracking transactions, managing payments, and closing your books easier. It uses AI to automate tasks that are usually done manually. Using it, you can quickly find details to solve problems and generate reports to meet financial rules like ASC 606, GAAP, SOX, etc.

Integrating NetSuite with Webgility lets you connect with Shopify, Amazon, Etsy, eBay, Lightspeed, Clover, Square, and other major sales channels. 

This integration also syncs order information in real time, allowing accurate financial records and inventory counts. It automates tasks like posting sales and managing product listings across different platforms.

Key features of NetSuite

• Automation of accounting processes: The software automates essential tasks such as invoicing, bank reconciliation, and expense tracking. 
  
  
• Real-time data access and reporting: NetSuite offers real-time insights into financial performance through customizable dashboards and reports. This feature allows managers to monitor key performance indicators (KPIs).
  
  
• Inventory and order management: It optimizes stock levels, tracks inventory in real time, and improves order fulfillment processes. This ensures that businesses can meet customer demands efficiently.

Benefits of integrating Webgility and Netsuite

• Enhanced tax and fee management: Webgility ensures you have all the data for precise tax filing across all sales channels. Furthermore, it seamlessly syncs fees from major payment processors, such as PayPal, Shopify Payments, and Stripe, and shipping fees from platforms like ShipStation and ShippingEasy.
  
  
• Multichannel inventory and price synchronization: Webgility transforms NetSuite into a centralized hub for inventory management. It allows you to synchronize inventory, pricing, and product information in real time across multiple ecommerce channels. This includes bidirectional price syncing, multi-location inventory management, and advanced serial.
  
  
• Automated product listings and purchases: The Webgility integration supports bulk product additions, automatic price and description syncing, and seamless product mapping across locations. For purchasing, Webgility generates purchase orders automatically based on inventory levels or shipping preferences, ensuring timely restocking and reducing operational bottlenecks.
  
  
• Comprehensive multichannel data syncing: Webgility securely syncs sales data from all your channels, including online stores, marketplaces, and POS systems. It also supports historical order syncing, ensuring that even past transactions are reflected in your NetSuite account. With SSL security protocols, businesses can trust the integration to keep their data safe while facilitating real-time updates.

Pros

• Offers a full suite of financial tools, including accounts payable, accounts receivable, general ledger, and tax management 
• NetSuite supports multi-currency transactions, global tax regulations
• Integrates with other systems, including customer relationship management (CRM), enterprise resource planning (ERP), and ecommerce platforms

Cons

• The platform’s extensive features can be overwhelming for new users
• It is expensive, especially for small businesses

Pricing 

NetSuite charges an annual license fee for the core platform, optional modules, and users, as well as a one-time setup fee. To get your tailored subscription, contact their support team.

3. Sage

Sage is an online accounting software for eBay sellers that offers real-time financial insights. Its AI-powered assistant, Sage Copilot, enhances productivity by automating tasks and providing personalized advice for informed decisions. The solution includes accounts receivable and payable, invoicing, inventory and order management, billing, cash management, and ledger accounting.

Key features of Sage

• Multi-currency capabilities: Sage supports transactions in multiple currencies, essential for sellers engaging in international trade. 
  
  
• Automated tax calculation: The software helps eBay sellers calculate sales tax accurately based on location, ensuring compliance with tax laws in different regions.
  
  
• Real-time profit and loss tracking: Sage provides real-time reports on sales, expenses, and profits. It thus gives sellers a clear view of their business performance at any given time.
  
  
• Expense tracking: Sellers can easily track expenses related to shipping, packaging, and eBay fees. This makes it easier to calculate profit margins.
  
  
• Inventory management: Sage helps manage stock levels by automatically updating inventory as sales are made, reducing the chances of overselling.
  
  
• Invoicing: The software allows eBay sellers to create professional invoices for their customers. This improves brand consistency and streamlining financial operations.
  
  
• Customizable reports: It offers customizable financial reports, allowing sellers to analyze their business performance in depth. Reports can include sales trends, tax liabilities, and more.

Pros 

• Sellers can generate detailed, tailored reports to track sales, profits, and tax liabilities.
• Automates tasks like bank reconciliation, inventory updates, and transaction 

Cons

• The software can be expensive for small businesses, with premium features requiring higher-tier plans.
• It lacks specialized features specifically for eBay sellers, such as detailed marketplace analytics or advanced shipping management.

Pricing

Here’s the Sage pricing plan:

• Pro Accounting: Priced at $625 per year for a single user
• Premium Accounting: Starts at $1,043 per year
• Quantum Accounting: Begins at $1,780 per year

4. Xero

Xero is eBay accounting software that centralizes business analytics, tracks project costs, manages invoices, and processes payments. Users can monitor real-time inventory, add items to invoices, and store files. Xero also streamlines bill payments, showing due dates and enabling batch payments. 

Key features of Xero

• Tax compliance: Xero simplifies tax management with automated VAT, GST, or sales tax calculations. It also supports filing tax returns directly with some jurisdictions.
  
  
• Automated reconciliation: This feature reconciles transactions by linking Xero to your business bank account or PayPal. Xero matches sales and expenses with your bank feed, saving you time.
  
  
• Inventory management: Xero tracks inventory levels, sets reorder points, and monitors product profitability. It helps you keep stock data accurate even as eBay sales occur.
  
  
• Invoicing and payments: The solution generates professional invoices for custom orders or services offered alongside eBay sales. You can integrate with payment processors like Stripe or PayPal for seamless customer payments.
  
  
• Multi-currency support: Xero’s multi-currency feature automatically calculates and records exchange rates, making it easier to manage global transactions.

Pros

• Supports multiple currencies for international transactions
• Updates financial data instantly for real-time tracking.
• Xero connects seamlessly with more than 1,000 third-party applications

Cons

• The basic plan has restrictions on the number of bills and invoices
• Some users experience syncing issues with bank feeds and transactions

Pricing

• Early Plan: $1/month 
• Growing Plan: $2.35/month 
• Established Plan: $4/month

Check Xero’s pricing page for the latest pricing.

5. Zoho Books

Zoho Books simplifies financial management and bookkeeping. It allows users to manage accounts payable and receivable, track inventory, and automate workflows. It enhances operational efficiency with features like customizable invoices, payment reminders, and integration with over 50 Zoho apps.

Key features of ZohoBooks

• Invoicing and billing: Users can effortlessly generate and send invoices, set up recurring billing, and manage customer payments. The software also allows users to customize invoice templates to reflect business branding.
  
  
• Banking integration: Zoho Books supports bank reconciliation by allowing users to connect multiple bank accounts and PayPal. Transactions are fetched automatically for easy reconciliation, helping to track cash flow and categorize transactions through customizable bank rules.
  
  
• Inventory management: This feature enables users to track stock levels, set reorder points, and manage purchase orders. It also provides alerts for low inventory and allows for adjustments in stock quantity and value.
  
  
• Reporting and analytics: With over 70 customizable reports, users can analyze their financial data effectively. These reports cover various aspects, such as sales performance, expenses, and project profitability.

Pros

• Supports international taxes and caters to eBay sellers operating globally
• Offers multi-currency functionality for seamless international transactions
• Provides comprehensive reporting tools tailored for eBay sellers
• Includes efficient sales tax management features

Cons

• Users might face a slight learning curve at the start
• Advanced features like automation are only available on higher-tier plans

Pricing

• Free Plan: Ideal for solopreneurs and micro businesses
• Standard Plan: $15/month
• Professional Plan: $40/month 
• Premium Plan: $60/month

Check Zoho’s pricing page for the latest pricing.

6. Wave Accounting

Wave Accounting offers essential features like invoicing, expense tracking, and basic reporting. It allows unlimited users and integrates with platforms like PayPal and Etsy. This makes it ideal for managing multiple online shops. 

Key features of Wave

• Financial reporting: Wave provides standard financial statements, such as Balance Sheets, Profit and Loss Accounts, and Cash Flow Statements. It also allows users to customize reports to track various financial metrics.
  
  
• Payroll management: Wave offers payroll processing, including tax filing and employee payment options via direct deposit.
  
  
• Invoicing and payment processing: You can generate unlimited invoices and email them directly to clients. It supports online payments through various gateways, including credit cards and bank transfers.

Pros

• Produces detailed sales tax reports and monitors tax-related data
• Provides unlimited tracking for both expenses and income
• You can customize invoice templates to suit your needs

Cons

• It offers fewer third-party integrations compared to some competitors
• The payroll functionality is restricted to users in the US and Canada

Pricing

• Starter Plan: Free ($0/month)
• Pro Plan: $16/month (Billed monthly)

Check Wave Accounting’s pricing page for the latest pricing.

Get Webgility to automate accounting on eBay

If you already use QuickBooks Desktop, QuickBooks Online, or NetSuite, Webgility is the missing link. It automates the updating of real-time data between your accounting software with eBay and other major ecommerce platforms like Amazon, Shopify, and POS systems. Webgility efficiently processes invoicing, expense tracking, payroll, and financial reporting, reducing manual entries.

Webgility key features

• Tax management: Webgility’s accurate sales data management helps with tax compliance. It can also integrate with Avalara to manage sales tax. This integration simplifies tax compliance, reporting, and filing processes by validating tax charges according to local regulations.
  
  
• Accounting automation: Webgility streamlines the real-time transfer of order and expense data between eBay and accounting tools like NetSuite or QuickBooks. This automatic synchronization ensures your financial records are always current. That means, Webgility makes it easier for you or your accountant to reconcile your finances quickly.
  
  
• Inventory management: It connects with QuickBooks or NetSuite Inventory to provide real-time inventory updates. This integration helps you avoid overselling and maintains stock levels by automatically generating purchase orders when necessary.
  
  
• AI assistance: With its AI Assistant (Beta), Webgility offers quick access to high-level financial insights, as well as the ability to retrieve order details, refunds, and product information instantly.

Testimonies

Here’s what G2 users said about using Webgility:

Conclusion

Accounting software like QuickBooks, NetSuite, Sage, Xero, and Zoho Books can help eBay sellers streamline their financial management and operations. They automate key tasks such as data synchronization, inventory management, expense tracking, and tax compliance.

For seamless financial reporting, you must consider software that features the following: expense tracking, eBay integration, real-time syncing, inventory management, tax compliance, and multi-currency support.

One of those software is Webgility, which integrates with NetSuite or QuickBooks accounting platforms. You’ll get multi-channel integration, real-time data syncing, advanced inventory management, and tailored financial reporting.

Start using Webgility today and experience seamless integration with QuickBooks or other platforms. Sign up now to streamline your eBay sales and financial management!