Over 50% of businesses struggle with manual accounting processes. If you’re a Magento store owner, the easiest way to escape this is by integrating accounting tools into your online store. Doing so will help streamline the accounting process.

Fortunately, Magento’s open-source platform facilitates accounting and automation through integrations. These tools can help you save time, reduce errors, and ensure accurate financial records, irrespective of whether you’re a small business or a large enterprise.

This article explores the best Magento accounting tools for optimizing your accounting workflow and enhancing your business’s financial accuracy.

Best Magento accounting tools to consider in 2025

1. QuickBooks Online/Desktop + Webgility 

QuickBooks is an excellent choice for Magento sellers because it automatically tracks finances, handles invoices, and manages inventory, giving accurate, real-time data. Also, it has customizable reports, tax tracking, and support for multiple currencies.

Although the solution QuickBooks has some ecommerce features, Webgility adds extra features to improve the overall experience. It syncs sales data, customer details, inventory changes, and financial transactions between QuickBooks and Magento. 

This reduces the need for manual work, reduces errors, and makes managing orders and financial reports easier for Magento sellers.

Key features of QuickBooks

  • Invoicing and Payments: Easily create and send professional invoices, track payments, and efficiently manage accounts receivable.
  • Expense Tracking: Keep track of and categorize expenses, link bank accounts for automatic transaction updates, and handle accounts payable seamlessly.
  • Financial Reporting: Generate detailed reports, including profit and loss statements, balance sheets, and cash flow statements, to gain valuable insights into your business performance.
  • Payroll Management: Manage employee payroll, calculate taxes, and ensure compliance with local regulations.
  • Inventory Management: Monitor inventory levels, manage orders, and track product costs to maintain optimal stock levels.

Benefits of integrating Webgility with QuickBooks 

Integrating Webgility with QuickBooks offers businesses a seamless way to manage their ecommerce operations and accounting. This integration benefits Magento users, providing automation, accuracy, and advanced analytics that enhance efficiency and decision-making. Below are the detailed benefits of this integration:

1. Automated posting of Magento Orders to QuickBooks

Webgility connects QuickBooks with your online stores, marketplaces, shipping platforms, payment processors, and point-of-sale systems, making it easy to sync and transfer orders directly into your accounting software. This allows you to create estimates, invoices, sales orders, or receipts.

With Webgility, you can:

  • Group Transactions: Combine multiple transactions into journal entries or line items, giving you control over how you categorize orders, no matter the payment method.
  • Magento Order Integration: Import Magento orders by date range or order status, so you can choose exactly which data to bring into QuickBooks.
  • Automation Rules: Set up rules to automatically download and post orders on a schedule that fits your business, reducing manual work.
2. Inventory synchronization

Webgility helps keep your product prices and stock levels updated across all sales channels, like Magento, QuickBooks, and any other platforms you use, whether online or in-person with a POS system.

It allows you to:

  • Scheduled Inventory Updates: Set up automatic updates for your inventory at your preferred times, ensuring everything stays in sync. This helps avoid overselling or mismatched stock levels.
  • Seamless Product Transfer: Easily move product data between QuickBooks and Magento. Keep your product details up-to-date, whether transferring info from your accounting system to your online store or managing listings.
  • Product Mapping: Link your products between Magento and QuickBooks to ensure consistent details and prices.
3. Tax, profit, and analytics tracking 

Webgility manages sales tax more efficiently by checking third-party tax calculations and directing the collected sales tax to the correct accounts, ensuring accurate payments.

It also offers a business analytics tool that combines data from all your sales channels into one easy-to-use platform. This lets you make smarter decisions and improve efficiency.

With Webgility, you can access:

  • SKU-Level Return Insights: See which products and sales channels have the highest return rates. It helps you spot trends and reduce losses from returns.
  • Revenue Forecasting: Use Webgility’s tools to predict future earnings to better plan for inventory, staffing, and marketing.
  • Interactive Heat Maps: View maps showing where your customers are shopping, giving insights into regional buying patterns.

Case Study:  How Rider Shack eliminated inventory errors between their Magento store and in-store sales using Webgility 

Problem

Rider Shack, a business managing both online and retail stores, faced significant challenges  QuickBooks Point of Sale. 

With over 13,000 products, the manual process of entering online sales into QuickBooks and syncing inventory between stores was time-consuming and error-prone. This resulted in stock-outs and customer dissatisfaction, as orders had to be canceled due to inventory discrepancies.

Webgility Integration 

Rider Shack implemented Webgility’s integration software alongside QuickBooks to overcome these issues. Webgility streamlined its inventory management by syncing data between its online store, retail store, and QuickBooks POS. 

Webgility also integrates with FedEx for shipping rate comparison and order tracking, simplifying processes like partial orders and instantly generating shipping labels.

Benefits

With Webgility, Rider Shack eliminated inventory errors, reduced inventory management time by 15 hours per week, and cut shipping processing time by 25%. 

The business now avoids out-of-stock issues and has saved an average of $1,400 per month in labor costs. The time saved allowed Rider Shack to focus on growing the business, improving customer experiences, and expanding product offerings. 

Key integrations

QuickBooks supports a range of integrations, through connector apps, that are particularly useful for Magento sellers, including:

  • Payment processors: PayPal, Stripe, and Square
  • Ecommerce platforms & marketplaces: Shopify, WooCommerce, and Amazon, eBay in addition to Magento
  • Shipping solutions: ShipStation, FedEx, and UPS
  • CRM systems: Salesforce and HubSpot

Check their integrations page for the full list of integrations.

Pros

  • Comprehensive feature set tailored for ecommerce businesses
  • Real-time synchronization of data across multiple platforms
  • User-friendly interface and customizable workflows
  • Excellent scalability to grow with your business

Cons

  • Initial setup may require a learning curve or the support of a bookkeeper or accountant.
  • Advanced features can be costly for small businesses

Pricing

QuickBooks Online variant has tiered subscription packages tailored to different businesses starting from $35/month.

2. Xero

Xero is another Magneto accounting integration that streamlines accounting and financial management processes. Sellers can easily track income and expenses, manage inventory, and generate financial reports. Also, It offers real-time insights into your Magento accounting report performance.

Key features

  • Real-time financial data: Xero allows businesses to access their financial information in real-time, providing instant insights into cash flow, expenses, and revenue.
  • Invoicing & payments: Users can create and send professional invoices, track payments, and accept online payments through the platform.
  • Bank reconciliation: Xero connects to your business bank account, allowing you to reconcile your transactions quickly and easily.
  • Multi-currency support: For businesses operating internationally, Xero offers support for multiple currencies, automatically converting foreign transactions into your home currency.
  • Inventory management: Xero helps businesses track inventory levels, manage product orders, and create reports related to stock levels.
  • Payroll: Xero’s payroll tools allow businesses to process employee salaries, deductions, and taxes quickly.
  • Tax compliance: Xero supports VAT, GST, and other local tax systems, ensuring businesses remain compliant with regulations and making tax calculations easier.

Pros 

  • Xero integrates with over 1,000 third-party apps.
  • The software handles multiple currencies.
  • It has a robust mobile application.
  • Xero updates financial data in real-time.

Cons

  • It doesn't provide a customer support phone number but will call you if necessary.
  • There are limits on bills and invoices with the entry-level plan.
  •  Some users experience issues with syncing bank feeds or transactions.

Pricing

Xero offers pricing plans with essential accounting features and flexible growth options. All plans come with 24/7 support, secure services, and a cancellation policy with one month's notice. 

  • Starter plan: $20/month 
  • Standard plan: $47/month 
  • Premium plan: $80/month

3. Sage

Sage helps Magento sellers automate financial tasks like invoicing, expense tracking, and tax calculations. It provides real-time visibility into cash flow, profit margins, and other key metrics, ensuring accuracy and efficiency in financial management.

Key features

  • Invoicing: Create, send, and track invoices easily. You can customize invoices, add branding, and automate recurring invoices.
  • Bank reconciliation: Connect your bank accounts to automatically import transactions and reconcile your bank statements in real-time.
  • Expense tracking: Track your business expenses by categorizing them and attaching receipts for easy record-keeping.
  • Financial reports: Generate financial statements like profit and loss reports, balance sheets, and tax reports with just a few clicks.
  • VAT management: Manage VAT easily, including VAT calculations, reports, and submissions to comply with local regulations.
  • Multi-currency support: Handle transactions in multiple currencies, ideal for businesses with international customers or suppliers.
  • Inventory management: Track stock levels, manage suppliers, and create purchase orders.
  • Payroll integration: Integrates with Sage Payroll, making it easier to manage employee payments, deductions, and taxes.

Pros 

  • Includes accounting, payroll, inventory management, tax compliance, and financial reporting tools.
  • Automates invoicing, bank reconciliations, and tax calculations, saving time and reducing errors.
  • Supports multi-currency transactions and compliance with international accounting standards.

Cons

  • Its advanced features can overwhelm users with no prior accounting experience.
  • The software can be expensive for small businesses, with premium features requiring higher-tier plans.

Pricing

Sage 50 provides several subscription plans:

  • 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. Wave Accounting

 

Wave Accounting is a Magento accounting extension offering various features, including invoicing, accounting, expense tracking, and financial reporting. The platform allows users to accept payments, create and send invoices, manage payroll, and generate reports to track business finances.

Key features

  • Expense tracking: Easily track business expenses by categorizing them and uploading receipts for better record-keeping.
  • Bank & credit card integration: Connect your bank and credit card accounts to import transactions and keep your records up to date automatically.
  • Financial reports: Generate detailed financial reports such as Profit and Loss, Balance Sheet, and Tax Reports to track the economic health of your business.
  • Receipt scanning: Use the mobile app to scan and store receipts directly, simplifying expense tracking and ensuring tax compliance.
  • Payment processing: Accept payments via credit card or bank transfer through Wave Payments, with low transaction fees.
  • Payroll (Additional Add-On Paid Feature): Wave offers payroll services for managing employee salaries, taxes, and filings. It is available in specific countries (mainly the U.S. and Canada).
  • Invoicing: Create professional invoices with customizable templates. You can also set up recurring invoices for regular clients.
  • Sales tax management: Track sales tax automatically and generate sales tax reports to comply with local tax laws.

Pros 

  • It generates sales tax reports and tracks taxes.
  • Wave offers unlimited expense and income tracking.
  • The solution provides fully customizable invoice templates.
  • Wave allows you to link your bank and credit card accounts.

Cons

  • Wave doesn’t have fewer third-party integrations.
  • Payroll feature is limited to the U.S. and Canada.

Pricing

Here is the subscription plan: 

Why should you use Webgility to automate accounting in Magneto?

Webgility is trusted by over 20,000 ecommerce businesses to integrate their QuickBooks Online, QuickBooks Desktop/Enterprise, and NetSuite seamlessly to Magneto and other ecommerce platforms like Shopify, BigCommerce, and marketplaces like Amazon, Walmart, eBay, and POS systems. 

This integration facilitates the automation of bookkeeping tasks for Magento store owners. It streamlines tasks such as invoicing, expense tracking, payroll processing, and financial reporting.

Webgility key features

  • Accounting automation: Webgility synchronizes order and expense data between Magento and accounting software like QuickBooks. This ensures that financial records are always up-to-date helping you or your accountant to reconcile finances in no time.
  • Inventory management: Webgility integrates with QuickBooks' inbuilt inventory to sync inventory in real-time. This prevents overselling and helps you maintain optimal stock quantities through automated purchase orders.
  • Tax management: Webgility integrates with Avalara for sales tax management. This feature ensures compliance with local tax regulations by validating sales tax charges based on jurisdiction, simplifying tax reporting and filing processes for you.
  • AI assistance: Webgility is the only QuickBooks connector app that has an AI agent out-of-the-box. You can pull high-level insights on your financials and instantly fetch order details, refunds, and product information.

Testimony

Here’s what a G2 user said about using Webgility:

“Webgility is an effortless software to operate. Its features are a boon, particularly when importing orders from multiple marketplaces into QuickBooks. The most significant advantage is that it eliminates the need for manual invoice entry. Customer support is unparalleled and is always available to answer queries or concerns. Additionally, the program can be customized to align with your personal preferences. If you sell packs on Amazon, this tool streamlines invoicing. We use this daily to import orders into invoices, saving us much time.”

Conclusion

Integrating accounting tools is essential for Magento store owners who aim to streamline financial management and foster business growth. By adopting efficient solutions like Webgility, store owners can seamlessly automate key accounting tasks, including tax management, inventory tracking, and reporting.

These tools save valuable time and ensure the accuracy of financial data. They empower businesses to focus on scaling and enhancing their operations.

Experience seamless accounting integration for your Magento store. Try Webgility today and simplify your accounting process.
John May John May
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