February 8, 2024
15 min

12 Best Accounting Software for Shopify in 2024 (Compared)

Do you have a Shopify store? Do you want to know the best accounting software for your needs? If so, read on to discover the best choice for you!
12 Best Accounting Software for Shopify in 2024 (Compared)
Table of contents

Managing your accounting can be a headache as a Shopify store owner. Did you know that an estimated 50% of small businesses fail within the first five years, often due to poor financial management? This blog aims to eliminate those odds with comprehensive guidance on top-tier Shopify accounting software.

Ready to transform your business finances for good?

Key Takeaways from this Post

Xero and QuickBooks Online are highly recommended options due to their user-friendly interfaces, robust features, and seamless integration with the Shopify platform.
With all the low-cost and free accounting options out there, you can keep on top of your books without the headache and hassle of spreadsheets.
Link My Books integrates with your accounting software to consolidate all of your Shopify sales and costs. Reconciliation of your monthly sales is quick, accurate, and simple.
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Best Shopify Accounting Software

Top Shopify Accounting Software Options

Two popular options of Shopify & eCommerce accounting software are Xero and QuickBooks Online.


Xero Pricing

Xero is a cloud-based accounting software tailored for small to medium-sized businesses. It offers a comprehensive suite of tools for Shopify that cater to various accounting needs, from invoicing to bank reconciliation. Xero's emphasis is on ease of use and mobile utility, making it a favorite among businesses that require real-time updates on the go.


  • Real-time Data Integration: Syncs across multiple devices, providing real-time updates.
  • Inventory Management: Helps businesses track their stock and manage inventory efficiently.
  • Payroll Integration: Via an integration with Gusto, it can handle payroll requirements.
  • Expense Tracking: Allows businesses to keep track of their expenses efficiently.
  • Sales Tax Calculation: Automated sales tax calculations for different regions.
  • Fixed Assets Management: Can manage assets like equipment, real estate, and more.


  • Unlimited users for all plans.
  • Hubdoc included in all plan tiers for automatic capture of receipts and bills.
  • Effective project tracking.
  • Comprehensive reporting capabilities.


  • Payment processing may lag for certain transaction types.
  • No automatic reminders for unpaid invoices.
  • No phone support.

Shopify Integration: Yes, it is an easy process to link, see here: Xero to Shopify

QuickBooks Online

QuickBooks PRicing

QuickBooks Online, developed by Intuit, is one of the most popular accounting platforms that cater to small business owners. It provides a clean, intuitive interface and a wide range of accounting tools, making it easy for even newcomers to manage their finances.


  • Mileage, Income, and Expense Tracking: All plans include these core features.
  • Sales and Tax Reporting: Provides comprehensive reports on sales and taxes.
  • Tools for 1099 Contractors: Helps manage payments and other details for contractors.
  • Inventory Management: Available with QuickBooks Online Plus and Advanced.
  • Third-party App Integration: Allows integration with various other tools and platforms.


  • Inventory management included with QuickBooks Online Plus and Advanced.
  • Double-entry accounting reports.
  • Wide range of tutorials, resources, and experts available online.
  • User-friendly interface suitable for both beginners and experts.


  • Monthly plans can be pricier than other accounting software options.
  • Each plan allows only a limited number of account users.
  • Advanced features may come with a learning curve.

Shopify Integration: Yes

Other Shopify Accounting Software Options

There are several other accounting software options available for Shopify sellers, providing a range of features and functionalities to meet different business needs.


Freshbooks pricing

FreshBooks is known for its user-friendly interface and comprehensive suite of features designed to make accounting tasks simpler and more efficient for small business owners and freelancers. It emphasizes automation in invoicing, expense tracking, and time management.


  • Intuitive interface and easy setup process.
  • Excellent customer support and a wide range of integrations.
  • Time-tracking and mileage tracking included in all plans.


  • Limited to a smaller number of billable clients in the lower-tier plans.
  • Lacks complex accounting capabilities for larger businesses.
  • No quarterly tax estimates directly from the platform.


  • Lite: Best for freelancers or small businesses, allowing invoicing up to 5 clients.
  • Plus: Offers more features, including unlimited invoices for up to 50 clients and automated recurring invoices.
  • Premium: Suitable for growing businesses, supporting unlimited invoices for an unlimited number of clients with advanced reporting tools.
  • Select: Custom plan for businesses that need lower credit card transaction rates, a dedicated account manager, and customized training for their team.

Shopify Integration: Yes


wave pricing

Wave provides a comprehensive, free accounting solution designed specifically for small businesses, freelancers, and consultants. It offers features like invoicing, accounting, and receipt scanning without any subscription fees.


  • Completely free to use, with no hidden costs.
  • Unlimited invoicing and accounting transactions.
  • User-friendly interface for easy navigation and setup.


  • Lack of direct payroll integration within all regions (payroll services are paid).
  • Limited customization options for financial reports.
  • Customer support options are limited to live chat for paid services.

Plans: Wave's accounting features are entirely free. Additional paid services include:

  • Payroll Services: Offers payroll in select countries, with pricing based on your country and the number of employees.
  • Payments Processing: Allows you to accept online payments from invoices or through the website, with transaction fees applicable.

Shopify Integration: No

Zoho Books

zoho pricing

Zoho Books is a comprehensive online accounting software designed for small to medium-sized businesses, offering a wide range of functionalities including invoicing, expenses, and inventory management.


  • Extensive features at a competitive price point.
  • Mobile app available for accounting tasks on the go.
  • Multicurrency support for global businesses.


  • The interface can be overwhelming for new users due to its extensive features.
  • Limited third-party integrations compared to competitors.
  • Advanced features such as project tracking require higher-tier plans.


  • Free: For businesses with annual revenue less than $50k. Includes basic features for invoicing and expense tracking.
  • Standard: Adds features like vendor credits, reporting tags, and up to 3 users.
  • Professional: Further includes purchase orders, sales orders, and inventory management.
  • Premium: Offers project billing, custom domain, and up to 10 users. Elite and Ultimate plans provide more advanced features for larger businesses.

Shopify Integration: Yes

Sage 50Cloud

sage pricing

Sage 50Cloud combines the robust accounting features of traditional Sage software with cloud mobility, offering advanced accounting capabilities, inventory management, and Microsoft 365 integration for small to medium-sized businesses.


  • Advanced inventory management and customization options.
  • Strong reporting capabilities with detailed financial insights.
  • Direct integration with Microsoft 365 for enhanced productivity.


  • The interface can feel outdated and less intuitive compared to other modern accounting software.
  • No native mobile app, limiting access on the go.
  • The learning curve for new users due to its comprehensive features.


  • Pro Accounting: Basic accounting features for small businesses, including invoicing, expense tracking, and financial reporting.
  • Premium Accounting: Adds advanced features like job costing, inventory management, and supports multiple users.
  • Quantum Accounting: Designed for larger businesses, offering extensive customization, advanced inventory features, and enhanced support.

Shopify Integration: No


kashoo pricing

Kashoo is an online accounting software designed for simplicity, targeting small business owners who need straightforward bookkeeping solutions. It emphasizes easy invoicing, expense tracking, and financial reporting with an intuitive interface.


  • Simple and straightforward interface, ideal for those new to accounting.
  • Machine learning technology for categorizing expenses and transactions.
  • Unlimited users, making it scalable for growing businesses.


  • Lacks some advanced features like time tracking and advanced inventory management.
  • No Android app, limiting mobile accessibility for some users.
  • Fewer integration options compared to other platforms.

Plans: Kashoo offers a straightforward approach with a single plan that includes all features:

  • Simple Plan: Provides access to all of Kashoo’s features, including invoicing, expense tracking, financial reporting, and unlimited users. Designed to offer everything a small business needs without the complexity of multiple plan options.

Shopify Integration: No


profiteer pricing

Profiteer is a specialized accounting software designed to help eCommerce businesses track and maximize their profits. It provides detailed insights into revenue, costs, and profitability margins with features that support real-time financial tracking and decision-making.


  • Real-time tracking of sales and profitability.
  • Customizable reports for detailed financial analysis.
  • Automated expense tracking to reduce manual data entry.


  • May be too specialized for businesses outside of eCommerce.
  • Limited integrations with third-party apps outside of Shopify.
  • Advanced features require the higher-tier plans.


  • Basic: Designed for startups, providing basic profit tracking and expense management.
  • Pro: Adds advanced financial analytics, multi-currency support, and custom reporting features.
  • Enterprise: Offers full customization, priority support, and integration capabilities for large eCommerce operations.

Shopify Integration: Yes


zarmoney pricing

Zarmoney offers a comprehensive cloud-based accounting solution that caters to businesses of all sizes, providing flexibility and scalability with a wide range of accounting and financial management tools.


  • Flexible and scalable accounting solution for all business sizes.
  • Extensive inventory management and time tracking features.
  • Customizable invoices and financial reports.


  • Learning curve for new users due to the extensive features.
  • Additional costs for multi-user access in the small business plan.
  • Limited mobile app functionality compared to competitors.


  • Entrepreneur: Basic accounting tools for individual business owners.
  • Small Business: Supports more complex operations with additional features like inventory management.
  • Enterprise: Full customization and advanced reporting for larger businesses with complex needs.

Shopify Integration: Yes


holded pricing

Holded is an all-in-one business management and accounting platform that simplifies operations, offering tools for invoicing, inventory, project management, and customer relationship management (CRM), designed for ease of use.


  • Comprehensive all-in-one platform for business management and accounting.
  • User-friendly interface with customizable dashboards.
  • Automated invoicing and real-time financial reporting.


  • Advanced features such as project management and inventory are available only in higher-tier plans.
  • Limited third-party app integrations.
  • CRM features could be more robust.


  • Starter: Essential tools for invoicing and basic accounting for freelancers and small businesses.
  • Standard: Adds inventory management, time tracking, and CRM functionalities.
  • Advanced: Comprehensive control

How to Choose the Best Shopify Accounting Software

To choose the best Shopify accounting software, consider factors such as pricing, features, user-friendliness, and integration capabilities with Shopify.

Selecting the Most Suitable Software

To choose the most suitable Shopify accounting software for your business, there are several important criteria to consider. 

Financial Management Capabilities

First and foremost, ensure that the software can effectively handle the financial management needs of Shopify sellers. Look for features such as inventory tracking, order management, and sales reporting specifically designed for eCommerce businesses.

Integration Capabilities

Next, consider the software’s integration capabilities. The selected software should seamlessly integrate with the Shopify platform to provide real-time data synchronization. This will streamline your operations and avoid manual data entry or discrepancies between systems.

Ease of Use and User Interface

Another crucial criterion is ease of use and user interface. Opt for a user-friendly accounting software that doesn’t require extensive training or technical expertise to navigate and operate effectively.

Comparison Table

Can’t decide? Here’s a quick and easy comparison table to help you make that final decision!

| Feature | Xero | QuickBooks | FreshBooks | Wave | Zoho Books | Profiteer | Zarmoney | Holded | ProfitBooks | OneUp | Sage 50Cloud | Kashoo | |-------------------------|:----:|:----------:|:----------:|:----:|:----------:|:---------:|:--------:|:------:|:-----------:|:-----:|:------------:|:------:| | Real-time Integration | 4.8 | 4.5 | 4.2 | 3.6 | 4.0 | 4.0 | 4.1 | 4.2 | 4.0 | 4.3 | 4 | 4 | | Inventory Management | 4.7 | 4.4 | 4.1 | 3.5 | 4.2 | 3.8 | 4.0 | 4.1 | 4.2 | 4.4 | 4.2 | 4.1 | | Payroll Integration | 4.5 | 4.3 | 4.0 | 3.4 | 4.1 | 3.9 | 3.8 | 4.0 | 3.7 | 4.1 | 4.4 | 3.9 | | Expense Tracking | 4.6 | 4.4 | 4.3 | 3.8 | 4.2 | 4.1 | 4.2 | 4.3 | 4.0 | 4.2 | 4.1 | 3.8 | | Sales Tax Calculation | 4.7 | 4.5 | 4.2 | 3.7 | 4.3 | 4.0 | 4.0 | 4.1 | 4.1 | 4.3 | 4.1 | 4.2 | | Fixed Assets Management | 4.6 | 4.2 | 4.0 | 3.6 | 4.1 | 3.7 | 3.9 | 4.0 | 3.8 | 4.0 | 4.2 | 4.3 |

Why Choose Xero or QuickBooks Online

Xero and QuickBooks Online are highly recommended for Shopify sellers due to their user-friendly interfaces, robust features, and seamless integration with the Shopify platform. These accounting software options provide efficient financial management solutions, allowing businesses to save time and accurately track their sales, expenses, inventory, and more in real time.

With Xero or QuickBooks Online as your chosen solution, you can streamline your accounting processes and make informed business decisions based on up-to-date financial data.

The Pros of Xero and QuickBooks Online

Xero and QuickBooks Online are two popular accounting software options for Shopify sellers. These platforms offer a range of benefits that make managing your finances easier and more efficient. 

With Xero, you can enjoy features like real-time data integration with your Shopify store, customizable invoicing templates, and automatic bank reconciliation. QuickBooks Online offers similar advantages, including easy inventory tracking, seamless integration with other apps, and the ability to create professional-looking financial reports.

Both Xero and QuickBooks Online provide user-friendly interfaces and robust reporting capabilities that can help streamline your financial management processes.

We Recommend a free trial for decision-making

To make an informed decision about the best Shopify accounting software for your business, it is recommended to take advantage of free trials offered by various providers. By trying out different options, you can assess their features and functionalities first-hand, allowing you to determine which software aligns best with your specific needs.

During the trial period, you can explore how efficient and user-friendly the interface is, as well as test its integration with the Shopify platform. This hands-on experience will give you a better understanding of each software's capabilities and help you choose the most suitable solution for managing your finances efficiently.

Transitioning from Spreadsheets to Accounting Software

PC Screen with Spreadsheet Software

Transitioning from spreadsheets to accounting software offers greater accuracy and time-saving benefits, making it a necessary step for Shopify sellers.

When to move away from spreadsheets

Many businesses find that it is time to move away from using spreadsheets for their accounting when they begin to experience inefficiencies and inaccuracies. Spreadsheets can be prone to human error, and as a business grows, the complexity of financial transactions increases.

This makes it difficult to manage finances effectively using spreadsheets alone.

By transitioning to accounting software, businesses can benefit from increased accuracy, streamlined financial management processes, and real-time data integration with platforms like Shopify.

Making the switch can save time and improve overall efficiency in managing finances for Shopify sellers.

Benefits of Using Accounting Software for Accuracy and Time-Saving

Implementing accounting software into your business operations can revolutionize how you manage your finances. 

The advantages extend far beyond mere automation, touching on crucial aspects like accuracy, time-saving, and overall efficiency. 

Here's a detailed look at how accounting software can be a game-changer for businesses aiming to streamline their financial processes.

Enhanced Accuracy

One of the most significant benefits of using accounting software is the remarkable increase in accuracy it brings to your financial management. Manual bookkeeping is prone to human error; even minor mistakes can lead to substantial discrepancies over time. Accounting software minimizes these errors by automating calculations and transactions, ensuring that figures are precise and reliable.

  • Automated Calculations: Software automatically handles all calculations, reducing the risk of human error in manual computations.
  • Consistent Data Entry: Predefined templates ensure that data is entered consistently, avoiding common mistakes that can occur with manual entry.
  • Real-Time Error Detection: Many accounting software solutions offer real-time alerts for any discrepancies or errors, allowing for immediate correction.

Time-Saving Efficiency

Accounting software significantly reduces the amount of time spent on routine financial tasks. By automating repetitive processes, businesses can allocate their resources to more strategic activities, enhancing productivity and growth.

  • Automated Transactions: Recurring financial transactions can be set up once and then processed automatically, saving countless hours.
  • Quick Access to Financial Statements: Generating financial reports can be done with a few clicks, eliminating the need for manual compilation and calculation.
  • Streamlined Invoicing: The invoicing process is expedited, with the software handling invoice creation, distribution, and even follow-up on overdue payments.

Improved Financial Control

With accounting software, businesses gain better control over their financial operations. The software provides detailed insights into financial performance, enabling informed decision-making.

  • Real-Time Financial Overview: Dashboards offer a real-time snapshot of financial health, including outstanding invoices, expenses, and overall cash flow.
  • Budget Management: Businesses can easily track their spending against their budget, ensuring that they stay on target.
  • Financial Forecasting: Advanced analytics tools within the software can predict future financial trends, aiding in strategic planning.

Enhanced Data Security

Financial data is sensitive and requires robust protection. Accounting software provides enhanced security measures to safeguard your data, reducing the risk of data breaches and unauthorized access.

  • Encrypted Data: Financial information is encrypted, making it unreadable to unauthorized users.
  • Access Controls: User permissions can be customized, ensuring that employees only have access to the information necessary for their role.
  • Secure Backup: Cloud-based accounting software offers secure, automatic backups, preventing data loss in case of hardware failure or other disasters.

Regulatory Compliance

Staying compliant with financial regulations is simplified with accounting software. The software is updated to reflect the latest tax laws and financial reporting standards, ensuring that your business remains in compliance without the need for constant manual updates.

  • Tax Compliance: Automatically calculates taxes based on the latest rates and rules, ensuring accurate tax filings.
  • Financial Standards: Software adheres to generally accepted accounting principles (GAAP) or international financial reporting standards (IFRS), as required

Benefits of using software for accuracy and time-saving

Using accounting software for your Shopify business offers numerous benefits, including increased accuracy and significant time-saving. With software, you can automate tedious tasks like data entry and reconciliation, reducing the risk of human error.

Additionally, the integration with the Shopify platform allows for real-time data updates, ensuring that your financial records are always up to date. By leveraging accounting software's efficiency and automation capabilities, you can streamline your financial management processes and focus more on growing your eCommerce business.

Problems with Using Spreadsheets for Shopify Accounting

Using spreadsheets for Shopify accounting can lead to a multitude of problems, including errors in data entry, difficulty in tracking expenses and revenue, lack of real-time updates, and time-consuming manual calculations.

Disadvantages of using spreadsheets

Using spreadsheets for Shopify accounting comes with several disadvantages. Firstly, spreadsheets can be prone to human error. Manual data entry and formula calculations increase the risk of mistakes, leading to inaccurate financial records.

Secondly, spreadsheets lack real-time updates and integration capabilities. This means that you may need to manually input and update data from your Shopify platform into the spreadsheet, resulting in inefficiency and possible discrepancies.

Lastly, as your business grows, managing a large volume of data in a spreadsheet becomes increasingly complex and time-consuming. This can hinder productivity and make it difficult to analyze your financial information effectively.

So in sum, that’s:

  • Human error
  • Lack real time updates & integration capabilities
  • Higher complexity & time-consuming

Key Benefits of Using Shopify Accounting Software

Using Shopify accounting software offers increased efficiency and accuracy compared to spreadsheets, streamlines financial management for Shopify sellers, and integrates seamlessly with the Shopify platform for real-time data.

Efficiency and accuracy compared to spreadsheets

Shopify accounting software excels in efficiency and accuracy, leaving traditional spreadsheets far behind. Using intelligent automation, it streamlines data input processes, saving considerable time and effort for Shopify sellers.

The risk of human error decreases significantly as the software accurately calculates taxes, monitors inventory levels, and prepares financial reports without manual intervention. This precision ensures dependable financial data that can guide effective decision-making for business growth.

With all figures instantly updated across systems and platforms, users have access to real-time information at any given moment — a feature spreadsheets can't match.

Streamlined financial management for Shopify sellers

Shopify accounting software facilitates swift and simplified financial management for e-commerce businesses. With novelty features like invoice generation, tracking expenses, calculating taxes, and inventory management, it reduces the manual labour involved in managing finances significantly.

Business owners can keep an eye on their cash flow with real-time data provided by these softwares.

The direct integration of this accounting software with Shopify stores is a huge advantage for sellers. It allows automatic syncing of sales data into the system, ensuring no discrepancies or errors due to manual entry.

This not only saves time but also helps in maintaining accurate business records which are crucial for making informed strategic decisions.

Integration with Shopify platform for real-time data

Shopify's accounting software seamlessly integrates with your platform, providing real-time data at your fingertips. This dynamic integration eliminates the need for manual data entry, significantly reducing errors and saving precious time.

With an updated financial snapshot always available, businesses can make informed decisions swiftly and confidently. The immediate access to key metrics like sales trends, inventory levels, and customer information ensures your business is agile and responsive to market changes.

Accurate financial reports are just a click away, simplifying end-of-year tax preparations or audits. Shopify makes handling finances easier than ever before by integrating effective accounting software into its platform!

Simplifying Shopify Accounting with Link My Books

Happy Accountant

Introducing Link My Books, an integration app that simplifies Shopify accounting with its user-friendly features and seamless integration. Discover how this tool can streamline your financial management and save you time and effort.

Introducing Link My Books

With Link My Books, you can say goodbye to manual data entry and spreadsheets, as it offers efficiency and accuracy compared to traditional methods. By automating the accounting process, this integration app helps save time and ensures that your financial records are always up-to-date.

Features and benefits of Link My Books

Seamless Integration with Shopify

Link My Books offers seamless integration with popular accounting software options like Xero or QuickBooks Online. This allows for smooth data transfer between platforms without the need for manual input or double entries.

Comprehensive Financial Management

Link My Books offers comprehensive financial management capabilities specifically designed for eCommerce businesses. Features such as inventory tracking, order management, and sales reporting help you effectively manage your finances.

User-Friendly Interface

Link My Books boasts a user-friendly interface that doesn’t require extensive training or technical expertise to navigate and operate effectively. This makes it easy for you to manage your finances without any hassle.

Time-Saving Automation

Link My Books automates many time-consuming tasks, such as reconciling transactions and generating reports. This saves you time and allows you to focus on growing your business.

Wrapping Up on Shopify Software

Using accounting software specifically designed for Shopify can greatly benefit eCommerce businesses and accountants. With its efficiency, accuracy, and integration with the Shopify platform, it streamlines financial management processes and provides real-time data insights.

Xero and QuickBooks Online are among the top options available, offering robust features and easy-to-use interfaces. 

Transitioning from spreadsheets to accounting software like Link My Books further simplifies Shopify accounting tasks while eliminating the problems associated with relying on manual calculations. 

You can also find free tools online like a Shopify calculator which take the guessing work out dealing with complicated Shopify Transaction Fees!

Overall, investing in a reliable Shopify accounting software is essential for optimizing financial operations and ensuring success in the ever-growing world of eCommerce.

Put your Shopify Accounting on Autopilot

Ready to simplify your Shopify accounting and take your business finances to the next level? Explore the top accounting software options mentioned in this blog post, such as Xero and QuickBooks Online.

Streamline your financial management processes, save time, and make informed decisions with real-time data integration.

Don't let poor financial management hold your business back—choose the right accounting software solution for your Shopify store today and pave the way for success! Start a 14 Day Free Trial Now!

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