
Effective financial management is crucial for success, and the eCommerce business is no different. To help online business owners and eCommerce entrepreneurs make informed decisions, we’ve curated a list of the best eCommerce accounting software options.
In this article, we’ll explore the features, benefits, and potential drawbacks of each software, empowering you to streamline your financial processes and optimize your reporting.
- eCommerce accounting software streamlines financial tasks specific to online businesses, from real-time inventory management to tax compliance
- Small business owners can leverage free accounting software options like Wave Accounting and Zoho Books, offering essential features without cost
- Invoicing software integrated with eCommerce accounting simplifies billing, enhances cash flow management, and supports growth
- Automation tools in accounting software reduce manual entry, errors, and the time spent on repetitive tasks
- Many solutions seamlessly integrate with popular eCommerce platforms, optimizing financial processes
- Accounting software can grow with your business, catering to the evolving needs of small business owners in the eCommerce sector
What Is eCommerce Accounting Software?
eCommerce accounting software is a vital tool for online businesses. These software solutions seamlessly integrate with your eCommerce platform, facilitating the efficient management and reconciliation of your sales, inventory, and expenses.
However, they are far more than just electronic ledgers. eCommerce accounting software is a robust and versatile tool that automates intricate processes, offers real-time financial insights, and ensures businesses adhere to tax laws, making it an indispensable asset for online entrepreneurs and business owners.
Types of eCommerce Accounting Software
Dedicated eCommerce accounting firm software serves as a crucial asset in the world of online business. It eases the burdensome and time-consuming task of number crunching and bookkeeping.
Whether you operate within a local market, on a national scale, or cater to a global audience, staying on top of taxes can often seem like a full-time job. The consequences of accounting and tax errors can be severe, leaving no room for shortcuts or rushed processes.
Here’s a breakdown of the types of eCommerce accounting software available:
- Cloud-Based Accounting Software: These solutions offer the flexibility of accessing your financial data from anywhere, allowing you to manage your eCommerce accounts conveniently.
- Integrated eCommerce Platforms: These are often bundled with eCommerce platforms, streamlining the accounting process by automatically syncing sales data with your accounting software.
- Specialized eCommerce Accounting Software: Tailored specifically for online businesses, these tools offer features designed to address the unique financial challenges and needs of eCommerce operations.
- Open-Source Accounting Software: These solutions provide customization options, allowing you to adapt the software to your specific eCommerce accounting requirements.
- Mobile Accounting Apps: With mobile accounting apps, you can manage your eCommerce finances on the go, ensuring you’re always in control, no matter where you are.
Why Your eCommerce Business Needs Accounting Software
Accounting software is indispensable for eCommerce businesses, primarily because they often contend with cash flow fluctuations driven by seasonality and promotional periods.
These tools play a pivotal role in helping you forecast cash flow, monitor liquidity, and ensure you maintain sufficient working capital for seamless operations.
From essential tasks like invoicing, billing, and tax calculations to more complex functions such as project management, accounting software serves as the backbone of your financial data management.
It allows you to efficiently handle clients, reconcile bank accounts, and generate insightful financial reports that foster the continuous and smooth growth of your eCommerce venture.
Here’s a list of what accounting software can be used for:
- Invoicing and billing: Create and send invoices to clients.
- Expense tracking: Monitor and categorize business expenses.
- Online payments: Facilitate secure online transactions.
- Bank reconciliation: Match transactions with bank statements.
- Timesheets and project management: Track employee hours and project progress.
- Tax compliance: Calculate, report, and file taxes accurately.
- Inventory Management: Keep tabs on stock levels and orders.
- Report generation: Generate financial reports for informed decision-making.
What to Look for When Selecting eCommerce Accounting Software
When it comes to selecting the right eCommerce accounting software for your online business, making an informed choice is paramount. The software you choose can significantly impact your financial management and reporting efficiency.
To ensure you make the best decision, consider the following key factors:
- Integration with Your eCommerce Platform: Seamless integration is vital. Ensure the software works harmoniously with your chosen eCommerce platform, allowing for easy data transfer and synchronization.
- Inventory Management: Effective inventory tracking is essential for eCommerce. Look for software that helps you monitor stock levels, track orders, and manage your supply chain efficiently.
- Real-Time Tax Calculations: Accurate and up-to-date tax calculations are crucial. Your software should automatically calculate taxes, ensuring compliance with ever-changing tax laws.
- User-Friendly Interfaces: A user-friendly interface simplifies the learning curve and ensures your team can navigate the software with ease.
These features are essential for optimizing your eCommerce accounting processes, so make sure the software you choose meets these criteria.
Best 11 eCommerce Accounting Software
Selecting the best eCommerce accounting software goes beyond mere convenience; it’s about seamless integration that eradicates the time-consuming tedium of duplicate data entry and the looming specter of costly mistakes.
QuickBooks Online

QuickBooks Online offers a robust eCommerce accounting solution with seamless integrations and free ProAdvisor support, making it a top choice for online businesses, but it comes at a higher cost and may not suit complex eCommerce operations.
- Seamless integration with popular eCommerce platforms like Shopify, WooCommerce, Magento, and BigCommerce
- New users can access free ProAdvisor support to set up their company.
- Ability to connect with additional eCommerce apps via services like Webgility, A2X, Connex, and Parex Bridge
- Automated sales tax calculations based on transaction location, along with the capability to file sales tax returns
- Relatively higher cost compared to some other small business accounting software options
- May not be suitable for managing complex eCommerce operations, such as advanced inventory management or detailed order tracking
- Compatibility with QuickBooks Commerce is limited to QuickBooks Online only
Plans & Pricing
- Simple Start: $30 per month for one user
- Essentials: $60 per month for three users
- Plus: $90 per month for five users
- Advanced: $200 per month for 20 users
New customers can enjoy either a 50% discount for the first three months or a 30-day free trial to explore the software.
NetSuite

Ideal for real-time tracking and multi-currency support, NetSuite is an excellent choice for businesses seeking comprehensive features like inventory tracking, forecasting, supplier management, general ledger, tax handling, data management, analytics, budgeting, and data visualization.
- User-friendly navigation simplifies platform usage
- Allows remote teams to access company data from anywhere
- Provides essential transaction tracking and monitoring reports
- Customization options can make the software complex for new users
Pricing
NetSuite eCommerce pricing varies based on feature requirements, typically falling within the range of $799 to $1,999 per month. Factors such as user count, the SuiteCommerce package chosen, and monthly transaction volume impact the overall cost of SuiteCommerce.
Zoho Books

Best for eCommerce companies seeking seamless Zoho integrations and robust mobile accounting, Zoho Books is a top choice among bookkeeping software for online businesses, offering accounting features comparable to QuickBooks and Xero, exceptional pricing, and excellent mobile functionality, including receipt capture, invoicing, and payment processing.
- Seamlessly integrates with various Zoho apps, creating a complete suite of management software
- Offers integration with numerous eCommerce apps via Zoho Flows, which does require a separate subscription
- Direct integration with popular eCommerce platforms like eBay, Shopify, Etsy, and Amazon through Zoho Inventory
- Limited eCommerce integrations unless subscribed to Zoho Inventory or Zoho Flows
- Lacks the capability to determine sales tax rates by location or file sales tax returns
Pricing
- Starter Plan: Begin with the free plan, suitable for solo users and accountants, ideal for businesses with annual revenues up to $50,000.
- Essential Plan: For just $20 per month, access the Standard plan, accommodating up to three users and serving 500 customers and vendors.
- Professional Plan: Upgrade to the Professional plan at $50 per month, extending usability to as many as five users.
- Premium Plan: At $70 per month, the Premium plan welcomes up to 10 users to streamline your operations.
- Elite Plan: Enjoy advanced inventory control and support for up to 10 users with the Elite plan, available at $150 per month.
- Ultimate Plan: Opt for the Ultimate plan, priced at $275 per month, providing space for up to 15 users, 25 custom modules, and advanced analytics to supercharge your eCommerce accounting.
Bench

Bench is a comprehensive, done-for-you bookkeeping solution, offering robust accounting visual reporting and the valuable addition of expert bookkeeper support when needed.
This platform is a lifeline for eCommerce businesses struggling to manage their financial tasks, with a team of experts working behind the scenes to maintain up-to-date and tax-compliant financial records. Bench doesn’t stop at bookkeeping; it also provides expert accounting advice to help users interpret the reports they generate.
- Impressive expense tracking tools
- Responsive email and phone support
- User-friendly interface for easy navigation
- Requires a learning curve to prepare reports
- May not connect with all business accounts
Plans & Pricing
- Essential Pricing: $249 per month (billed annually) or $299 per month (billed monthly)
- Premium Pricing: $399 per month (billed annually) or $499 per month (billed monthly.
A2X

A2X is a cloud-based eCommerce accounting solution, offering the seamless transfer of transactional data from sales platforms like Shopify, BigCommerce, and Amazon.
A2X’s integrations with popular eCommerce accounting software, including Xero and QuickBooks, simplify the transition of financial records, acting as the crucial link to streamline your back office operations and open up new possibilities.
- User-friendly interface, making it easy to navigate
- Offers straightforward and efficient integrations
- Provides an intuitive user experience
- The setup process may have a learning curve
- Customer support requires improvement
Plans & Pricing
- Mini Plan: $19 per month
- Basic Plan: $39 per month
- Pro Plan: $69 per month
- Advanced Plan: $99 per month
Wave Accounting

Wave Accounting is a popular choice due to its unique offering of free accounting and invoicing features. Users benefit from sending unlimited customer invoices, setting up multiple organizations, and comprehensive account tracking at no cost.
The platform also integrates bank reconciliation for real-time transaction tracking by linking bank accounts, PayPal, and other data sources.
- Effortless management of invoices and annual accounting
- Capacity to handle multiple businesses
- Intuitive and user-friendly platform
- Users can’t download monthly reports
- Customer support requires enhancement
Pricing
- Free option for invoicing and accounting
- Credit card fees starting at 2.9% plus $0.60 per transaction
- Mobile receipts at $8 per month
- Payroll services for $40 per month
- Bookkeeping support for $149 per month
Multiview ERP

Multiview ERP is an enterprise resource planning tool that serves as a unified source of truth, enhancing visibility into accounting data. With robust features like a powerful general ledger, it provides timely access to essential financial information.
Multiview ERP’s business intelligence tools enable users to dive deep into financial data through customizable dashboards and accounting statements.
- Exceptional customization capabilities
- Reports offer comprehensive information summaries
- Provides strong customer support
- Learning curve can be steep
- The navigation can be complex
Pricing
Multiview ERP employs a tiered pricing structure, with annual billing for all businesses. Pricing models vary based on the selected software version, typically with the Standard version being more cost-effective compared to the Enterprise version, reflecting differences in feature access. Licensing is based on user count.
Xero

Xero is a robust accounting solution comparable to QuickBooks, offers extensive accounting features, albeit with slightly less seamless eCommerce integration. While it directly integrates with Shopify and interfaces with Zapier, third-party connectors like A2X and Parex Bridge are needed to integrate with platforms such as WooCommerce, Amazon, and Etsy.
- Direct integration with Shopify
- Support for integration with third-party connectors like A2X and Parex Bridge
- Strong inventory accounting capabilities
- More cost-effective than QuickBooks, with unlimited users in all plans
- Sales tax rates must be manually set for each location with a taxable sale
- Inability to file sales tax returns directly through the platform
- Fewer independent Xero-certified bookkeepers compared to QuickBooks
Plans & Pricing
- Xero Early: $15 per month, offering 20 invoices and five bills
- Xero Growing: $42 per month, providing unlimited invoices and bills
- Xero Established: $78 per month, featuring support for multiple currencies
Xero offers new users the choice between a 50% discount for two months or a 30-day free trial with no credit card required.
Kashoo

Kashoo is a straightforward accounting software that simplifies business financial management. It offers essential features, including recurring invoicing and seamless bank and credit card account connections for swift reconciliation.
Kashoo accommodates multiple businesses within a single system, making it easy to oversee various enterprises.
- Swift and user-friendly interface
- Cloud-based, ensuring accessibility from anywhere
- Simple implementation process
- Reporting features may require improvement
- The mobile app lacks robustness
Plans & Pricing
- Truly Small Accounting: Priced at $216 per year
- Kashoo: Available at $324 per year
Acumatica Cloud ERP

Acumatica Cloud ERP empowers users with extensive customization capabilities, enabling precise alignment with their accounting needs. Those with skilled developers can further tailor processes and leverage AI and machine learning technologies to suit their eCommerce operations.
Acumatica stands ready to scale with your growing business, seamlessly integrating with your online store’s workflow.
- User-friendly interface
- Modular platform design
- Comprehensive customization options
- Complex report creation
- Confusing search function
Pricing
In terms of pricing, determining the cost of an ERP system depends on specific needs and factors. ERP applications are intricate, and the pricing structure varies. It’s essential to partner with Acumatica to assess individual requirements to get a more accurate pricing estimate.
ERP applications are complex and there are many factors that need to be considered before a final price can be given.
OneUp

OneUp, a versatile small business accounting application, caters to sole proprietors, freelancers, and growing businesses alike. Surprisingly affordable, it boasts a robust feature set, encompassing lead management for tracking potential customers and an impressive inventory module. This platform provides comprehensive accounting functionality, allowing users to connect their financial institutions.
What sets OneUp apart is its flexibility; users can manually enter accounting transactions, a feature not found in similar applications like Wave Accounting or Xero. Other functionalities include sales and vendor quotes, purchase orders, and credit memos.
While vendor payments can be tracked, there’s no direct payment option through the application. Users can record payments and specify the bank account used.
- All plans offer the same feature set
- The mobile app provides access to all application features
- Suited for small businesses and those in the growth phase
- Reporting options could be more extensive
- Lack of telephone support
- No bill payment option offered
Pricing
OneUp’s pricing structure is user-based, ensuring access to the same features across all plans. The Self (single user) plan is priced at $9 per month, while the Team plan costs $69 per month. Scaling up is necessary only to add users, not to access additional features.
How to Choose the Best Accounting Solutions for eCommerce?
Choosing the right accounting solution for your eCcommerce management is a critical decision that can greatly impact the efficiency of your online store, particularly in areas like inventory management.
Here’s a step-by-step guide to help you make an informed choice:
- Identify Your Specific Needs: Begin by understanding the unique needs of your eCommerce business. Consider factors like the volume of transactions, the complexity of your inventory, and the level of integration required with your online store.
- Budget Considerations: Determine your budget. Accounting solutions come with a range of pricing options, so it’s important to find one that aligns with your financial resources.
- Integration Compatibility: Check if the software seamlessly integrates with your eCommerce platform. Ensure that it can manage sales, inventory, and expenses without creating duplicate entries.
- Scalability: Assess the scalability of the software. Your eCommerce business may grow, and the accounting solution should be capable of accommodating this expansion.
- User-Friendliness: Evaluate the user interface. User-friendly software can reduce the learning curve for you and your team, ensuring that you can easily navigate and utilize its features.
- Reporting and Analysis: Look for software that provides robust reporting and analysis tools. These are essential for monitoring your ecommerce financial performance.
- Tax Compliance: Ensure that the software can handle tax calculations and reporting effectively, particularly if your online store operates in multiple locations.
- Customization: Some eCommerce businesses may require specific customizations. Choose a software that offers flexibility for tailoring to your unique needs.
- Customer Support: Consider the level of customer support provided by the software provider. Access to timely and reliable support can be crucial in addressing any issues that may arise.
- Free Trials and Demos: Whenever possible, take advantage of free trials or software demos. This hands-on experience can help you determine if the software aligns with your requirements.
By following these steps, you can select the best accounting solution for your eCommerce business, ensuring efficient financial management, inventory tracking, and seamless integration with your online store.
How Does eCommerce Accounting Software Differ from Traditional Accounting Software?
eCommerce accounting software differs from traditional accounting software by offering specialized features for online businesses, such as seamless integration with eCommerce platforms, inventory management tailored to the demands of digital sales, and automated tax calculations for various transaction locations.
It adapts to the dynamic and transaction-heavy nature of online stores, ensuring efficient financial management specific to the eCommerce sector.
What Are the Benefits of eCommerce Accounting Software?
eCommerce accounting software streamlines financial processes for online businesses, offering benefits like real-time sales and inventory tracking, simplified tax management, and automated report generation.
It minimizes manual data entry, reduces errors, and enhances decision-making with insightful financial analysis. It caters to the unique needs of ecommerce, facilitating efficient financial management, and helping businesses stay competitive in the online market.
How Can Accounting Software Help Scale My Online Business?
Accounting software aids in scaling your online business by automating financial tasks, offering real-time insights into sales and expenses, and ensuring accurate inventory management. It facilitates streamlined operations as your business grows, preventing financial bottlenecks.
Automated reporting and analysis enable data-driven decisions, while the ability to integrate with eCommerce platforms allows seamless expansion. This promotes efficient scalability and sustainable growth.
Will Accounting Software Integrate with my eCommerce Platform?
Most modern accounting software options offer integration with popular eCommerce platforms such as Shopify, Wix, and WooCommerce. They can sync with online stores, streamlining financial processes by automatically importing sales, expenses, and inventory data.
However, the level of integration may vary, so it’s important to choose software that aligns with your specific eCommerce platform and provides seamless synchronization, reducing manual data entry and the risk of errors.
Can You Use Shopify as an Accounting Software?
While Shopify provides some financial reporting features, it’s not a comprehensive accounting software. Its basic plan offers finance reports and limited inventory insights but lacks sales and profit reports.
As your business expands, you’ll likely require more robust accounting software to facilitate long-term planning and comprehensive financial management.
Is There Any Free eCommerce Accounting Software Available?
Yes, there are free accounting software options available. Wave offers completely free accounting and invoicing tools. Zoho Books, part of the Zoho suite, offers a free version with essential features like expense tracking, reconciliation, invoices, and email support, making it a cost-effective choice for getting your finances in order.
When Should an eCommerce Business Use an Accountant?
eCommerce businesses should consider hiring an accountant when they face complex financial tasks, such as managing multi-channel sales, navigating intricate tax regulations, or needing specialized advice on optimizing their financial strategies.
Accountants can also be valuable during periods of rapid growth, business restructuring, or when financial errors need expert resolution, ensuring compliance and effective financial management.
Conclusion
Selecting the right eCommerce accounting software is crucial for efficient financial management in the digital marketplace. These specialized tools streamline processes, enhance inventory control, and provide real-time insights, helping your online business thrive.
For further guidance on optimizing your eCommerce operations, explore the best eCommerce platforms and eCommerce hosting solutions.
Next Steps: What Now?
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- Learn how to Build an eCommerce Website
- Understand the Metrics to track for website success
- Find out how to Use AI in Your eCommerce Business
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