Best accounting software for Shopify: 5 excellent options to consider.

Shopify has gained a reputation as an ecommerce powerhouse, with over one million businesses using its site builder and point-of-sale services. With its affordable platform and robust business management tools, it’s no surprise many merchants get started with Shopify.

But even the best business software can’t do it all. Accounting software fills in the gaps, letting you track business expenses and income, run reports, prepare for tax time, send and receive payments, and more. 

Hopefully, you’ve already registered your business, opened a business bank account, and have your business records in order, so you’re ready to sign up for accounting software.

Now, it’s time to go comparison-shopping. Here are five top options offering the best accounting software for Shopify.

Best accounting software for Shopify store owners.

All of the accounting software options we’ve compiled are cloud-based, which means you can access your data anytime, anywhere, from any device connected to the internet. Cloud solutions help you avoid manual data entry mistakes that are easy to make when you’re copying over sales figures and other information.

One important note: Most accounting software doesn’t directly integrate with Shopify. You may have to find an app connector in the Shopify App Store, or use apps like Zapier and A2X to set up the integration. Most apps include easy-to-follow instructions, so you can manage setup without calling a software developer. 

1. doola

Description:

doola is an all-in-one platform that simplifies launching and managing U.S.-based LLCs and C Corps for founders globally. It simplifies the back-office and streamlines business formation, bookkeeping, tax compliance, and analytics, allowing founders to focus on growth. Backed by Y Combinator, doola serves over 10,000 entrepreneurs globally.

Key features:

• Business formation: Handles LLC and C Corp formation in all 50 U.S. states, including EIN acquisition registered agent services, and US business bank account setup for non-residents.
• Bookkeeping solution: Provides real-time financial tracking, ecommerce analytics, and dedicated bookkeeping support for Shopify and Amazon sellers.
• Tax compliance: Manages federal, state, and sales tax filings, including Form 1099 and reseller certificates, to ensure compliance and avoid penalties.
• Analytics dashboard: Offers real-time sales, order, and financial insights for ecommerce businesses, with Shopify and Amazon integrations.

Pros:

• Designed for both U.S. and non-U.S. residents, enabling global entrepreneurs to start U.S. businesses without an SSN or physical presence.
• Comprehensive all-in-one solution combines formation, bookkeeping, taxes, and analytics, eliminating the need for multiple vendors.
• Tools for ecommerce, like sales tax compliance and analytics, streamline operations for Shopify and Amazon sellers.
• 30-day free trial on bookkeeping and analytics software

Cons:

• Monthly pricing can be higher than DIY options
• No mobile app (web-based only)
• Analytics currently limited to Shopify and Amazon, with additional platform integrations still in development.

Pricing:

doola offers tiered pricing based on the level of service you need. The Starter Formation Package is $297 plus state fees and includes LLC setup, EIN, and a registered agent for the first year. For a more comprehensive offering, the Total Compliance Plan is $1,999/year and includes tax filings, compliance support, analytics, and more. Their premium Business-in-a-Box package ($2,999/year or $329/month) includes dedicated bookkeeping, CPA tax filings, and access to all analytics tools — ideal for growing ecommerce businesses. All plans come with transparent pricing and no hidden fees.

2. QuickBooks Online

Description:

QuickBooks Online is an industry-leading cloud-based accounting software trusted by millions of small and medium-sized businesses worldwide. It delivers robust financial management tools, extensive reporting capabilities, and scalable solutions suitable for Shopify stores looking for advanced bookkeeping, integrations, and automation.

Key Features:

• Automated bookkeeping: Automatic transaction categorization, expense tracking, and bank reconciliation.
• Ecommerce integration: Connects seamlessly with Shopify through official apps or third-party connectors, automatically syncing sales, fees, and payouts.
• Financial reports: Detailed and customizable reports (profit and loss, balance sheets, cash flow statements) in real-time.
• Inventory management: Integrated tools for managing stock levels, sales orders, and purchase orders.

Pros:

• Widely adopted, making it easy to find accountants familiar with the platform.
• Strong automation capabilities significantly reduce manual data entry.
• Scalable plans support business growth from small to medium-sized enterprises.
• Vast ecosystem of integrations, including Shopify, PayPal, and other popular platforms.

Cons:

• May require third-party apps for Shopify integration.
• Higher subscription tiers can become costly as your business scales.
• Steeper learning curve for users new to accounting software.

Pricing:

QuickBooks Online pricing starts around $35/month for the Simple Start plan (single user) and scales up to approximately $235+/month for Advanced plans supporting multiple users, advanced reporting, and inventory management. A 30-day free trial is typically available.

3. NetSuite (Oracle NetSuite)

Description:

NetSuite by Oracle is a powerful, cloud-based ERP solution that goes beyond accounting to offer a unified platform for managing financials, operations, and inventory for rapidly scaling Shopify stores and multi-channel ecommerce businesses. Ideal for enterprises or complex Shopify operations requiring robust financial control, analytics, and integration capabilities.

Key features:

• Unified financial management: An accounting suite including general ledger, accounts payable/receivable, and sophisticated financial reporting.
• Advanced inventory management: Real-time visibility into inventory across multiple sales channels, automated replenishment, and multi-location tracking.
• Business intelligence: Integrated analytics and real-time dashboards for deep business insights and strategic decision-making.
• Customizable workflows: Highly configurable to match complex operational needs, supporting detailed processes across financial and operational management.

Pros:

• Scalable ERP solution handling complex business processes effortlessly.
• Powerful analytics and real-time financial reporting provide actionable business insights.
• Robust integration ecosystem supports extensive Shopify connectivity via third-party connectors like Celigo and FarApp.
• Ideal for rapidly scaling Shopify stores expanding into multiple sales channels or international markets.

Cons:

• High cost of licensing, implementation, and ongoing support.
• Complex implementation requiring technical resources or consultants.
• Steep learning curve; typically requires dedicated accounting staff or ERP administrators.

Pricing:

NetSuite pricing is custom-quoted, typically starting at several thousand dollars per year. Costs vary based on business size, modules selected, and number of users. Setup and implementation fees often apply, and consultation is recommended.

4. Xero

Description:

Xero is a popular cloud-based accounting solution valued for its intuitive, user-friendly interface and strong international capabilities. Shopify merchants particularly appreciate Xero for streamlined bookkeeping, easy collaboration with accountants, and integrated multi-currency support—essential for global ecommerce stores.

Key features:

• Cloud accounting: Intuitive, easy-to-use dashboards accessible from any device.
• Shopify integrations: Facilitates sales data synchronization via third-party apps (like A2X) and automated bank reconciliation.
• Unlimited users: Allows access to accountants, business partners, and employees without extra costs.
• Multi-currency support: Ideal for global Shopify stores handling transactions in various currencies seamlessly.

Pros:

• Easy to use, ideal for business owners without extensive accounting knowledge.
• Strong multi-currency functionality supporting international ecommerce.
• Unlimited users on all plans, beneficial for collaborative businesses.
• Extensive third-party app marketplace enhancing Shopify integration and functionality.

Cons:

• No direct native Shopify integration; requires third-party connectors for automated data syncing.
• Entry-level plans have limitations on invoicing and bank transaction volumes.
• May require supplementary apps for ecommerce accounting features.

Pricing:

Xero offers tiered subscription plans: Starter ($20/month, limited features), Standard ($47/month, full accounting), and Premium (~$80/month, advanced multi-currency features). A 30-day free trial is usually available.

5. FreshBooks

Description:

FreshBooks is a user-friendly cloud-based accounting software specifically suited for smaller Shopify stores, freelancers, and service-oriented businesses. Known for exceptional invoicing capabilities and ease of use, FreshBooks simplifies expense tracking, financial management, and billing processes, even for users with limited accounting experience.

Key features:

• Intuitive invoicing: Professional invoice creation, automated reminders, and built-in payment acceptance.
• Expense tracking: Automatic categorization, receipt scanning via mobile app, and real-time expense reporting.
• Time tracking: Built-in timer and billing tools beneficial for service-based Shopify businesses.
• Third-party Shopify integrations: Sync sales data using apps like Zapier, enabling basic automation.

Pros:

• Highly intuitive interface designed for non-accountants.
• Robust invoicing tools and automated billing features.
• Mobile-friendly platform ideal for managing finances on-the-go.
• Excellent customer support, often praised by small business users.

Cons:

• Limited ecommerce-specific features; primarily aimed at freelancers and small businesses.
• Shopify integration relies on third-party connectors rather than native apps.
• Pricing tiers restrict features like multi-user access and advanced accounting functions.

Pricing:

FreshBooks offers tiered plans starting at approximately $21/month (Lite plan, 5 clients), around $38/month (Plus, 50 clients), and about $65/month (Premium, unlimited clients). A 30-day free trial is typically provided.

Factors to consider when selecting a Shopify accounting solution

Choosing the right accounting software for your Shopify store requires careful evaluation of multiple factors that extend past basic bookkeeping capabilities. The ideal solution should align with your business size, technical expertise, and growth plans while providing the automation needed to minimize manual data entry.

Integration & automation

The depth of Shopify integration should guide your selection of accounting software. When evaluating platforms, prioritize those that offer real-time syncing of orders and payouts. This automation transforms hours of manual data entry into a background process that runs while you focus on growing your business.

Direct integration capabilities vary significantly across platforms. QuickBooks and Xero require third-party connectors like A2X to automate Shopify sales data effectively. While this adds complexity and cost, the combination captures every transaction detail, from sales tax to shipping fees. Services like doola Books provide native Shopify integration designed specifically for e-commerce businesses, eliminating the need for additional connectors. Some platforms offer only basic connectivity and require manual intervention to reconcile transactions accurately.

Consider how each platform handles e-commerce accounting nuances. Does it automatically categorize Shopify fees? Can it distinguish between product sales and shipping revenue? The best solutions intelligently parse your Shopify data, creating proper journal entries without constant oversight. When you choose accounting software for Shopify, the quality of integration often determines whether bookkeeping becomes a manageable task or a time-consuming burden.

Business size

Your current operation and growth trajectory should heavily influence your software selection. A new Shopify seller operating from home has fundamentally different needs than an established brand processing thousands of orders monthly across multiple sales channels.

Solo entrepreneurs just starting out often benefit from prioritizing simplicity over sophistication. Free or low-cost options can handle straightforward operations adequately. These entry-level platforms offer enough functionality to maintain compliance and understand your financial position without overwhelming features you won't use.

As transaction volumes increase and operations become more complex, entry-level limitations become apparent. Fast-scaling brands often need robust inventory tracking, detailed financial reporting, and multi-currency capabilities for global expansion. Mid-tier solutions like Xero or QuickBooks Online Advanced offer the scalability to grow alongside your business.

Enterprise-level operations or those with complex supply chains may require ERP systems like NetSuite. These platforms handle high transaction volumes, multiple warehouse locations, and sophisticated revenue recognition requirements that simpler tools cannot manage effectively.

Features needed

Before evaluating any Shopify accounting software features, create a list of your must-have capabilities. This exercise prevents you from being swayed by impressive but unnecessary functions while ensuring you don't overlook essential functionality.

Inventory management represents a key decision point. If you rely on Shopify's native inventory tracking or specialized apps, you may not need robust inventory features in your accounting software. However, businesses managing inventory across multiple channels often benefit from accounting platforms with integrated inventory modules. Sage 50 offers sophisticated inventory forecasting that helps prevent stockouts and optimize purchasing decisions.

Multi-currency support becomes essential for international sellers. Xero excels here, automatically updating exchange rates and handling foreign currency gains and losses. Advanced reporting needs might push you toward platforms like QuickBooks Online Advanced, which offers customizable financial statements and detailed analytics. Consider whether you need project costing, time tracking, or industry-specific features that could narrow your options.

Ease of use

The most feature-rich software becomes worthless if you and your team avoid using it due to complexity. User experience significantly impacts whether you'll actually maintain accurate books or let them fall behind.

FreshBooks and similar user-friendly platforms built their reputations on intuitive interfaces that non-accountants can navigate confidently. Their streamlined dashboards and straightforward invoice creation make daily tasks manageable for time-strapped entrepreneurs. These platforms sacrifice some advanced functionality for accessibility, a trade-off that works well for many small businesses.

NetSuite offers tremendous power but requires significant training to use effectively. Many businesses implementing NetSuite budget for extensive onboarding and ongoing support. Between these extremes, platforms like QuickBooks Online and Xero balance professional-grade features with interfaces most users can master within weeks rather than months.

Consider not just your own comfort with technology but who else will use the system. If you plan to delegate bookkeeping tasks to employees or virtual assistants, platforms with gentler learning curves reduce training time and errors.

Budget

The true cost of accounting software extends well past monthly subscription fees. When seeking the best bookkeeping solution for your Shopify store, factor in all associated expenses to understand the total investment required.

Entry-level and free-tier options attract many new sellers, and for basic operations, they can suffice. However, once you need features like automatic bank reconciliation or professional support, costs accumulate. Mid-tier options like QuickBooks Online or Xero typically range from $25 to $80 monthly, but remember essential add-ons. A2X costs $19 to $149 monthly depending on order volume, potentially doubling your accounting software costs.

Enterprise solutions like NetSuite require a different budget mindset. Implementation alone costs thousands of dollars, with monthly fees often exceeding $1,000. However, for businesses at scale, efficiency gains and reduced manual processes can deliver substantial ROI.

Don't overlook the human element in cost calculations. Complex software might necessitate hiring a specialized bookkeeper or paying for additional training. Conversely, investing in more expensive but user-friendly software could eliminate outsourced bookkeeping entirely, potentially saving money long-term.

Support and resources

When technical issues arise or you need help understanding features, the quality of available support becomes paramount. The landscape varies dramatically across providers.

QuickBooks and Xero benefit from massive user communities and extensive third-party support networks. Thousands of accountants specialize in these platforms, making it easy to find professionals familiar with your chosen software. Both companies offer direct support, though response times and quality vary based on subscription tier.

Some platforms rely primarily on community forums and help articles rather than direct support. While user communities can be helpful, complex issues might leave you searching for answers independently. Consider whether your accountant or bookkeeper already works with specific platforms—many professionals readily support QuickBooks or Xero but have less experience with newer or niche options.

Banking and payment integration

Modern financial operations require seamless connections between banking, payment processing, and accounting systems. If you use business banking solutions like Brex, ensure your accounting software can integrate to import expenses automatically—many popular options do via Brex's integrations. This connectivity eliminates manual expense entry and reduces the risk of missing deductible business expenses.

The quality of bank feeds and transaction matching capabilities varies significantly across platforms. Superior integration means less time categorizing transactions and more accurate financial records. As you evaluate options, consider how each platform handles your specific banking relationships and whether it supports your preferred payment methods and expense management tools.

Focus on growing your business, not lost receipts

Selecting the right accounting software for your Shopify store is not a decision to take lightly. As we've explored, the landscape ranges from simple, affordable solutions suitable for solo entrepreneurs to sophisticated ERP systems designed for complex, multi-channel operations. The key lies in honestly assessing your current needs while anticipating future growth. Whether you opt for the native e-commerce focus of doola, the widespread adoption of QuickBooks, or the international capabilities of Xero, your choice should reflect both your operational complexity and your team's technical capabilities.

The true value of proper accounting software extends far beyond mere compliance. The right platform transforms financial management from a dreaded monthly task into a strategic advantage. It provides real-time insights into profitability, automates tedious data entry, and creates audit trails that protect your business during tax season. Most importantly, it frees you to focus on what matters most: growing your Shopify store. The hours saved through automation and the errors avoided through proper integration quickly justify the investment in quality accounting software.

For e-commerce companies seeking to streamline their entire financial stack, modern business banking solutions like Brex offer compelling advantages that complement your accounting software choice. Brex provides corporate cards with built-in expense management and accounting automation software that seamlessly integrates with major platforms including QuickBooks, Xero, and NetSuite. This creates a unified financial ecosystem where every transaction flows automatically from card swipe to accounting entry, eliminating manual expense reports and ensuring nothing falls through the cracks. The real-time visibility into spending, combined with powerful controls and rewards tailored for business purchases, makes Brex particularly valuable for growing Shopify stores managing multiple team members and vendors. With Brex's accounting automation handling the heavy lifting of categorization and syncing, your team can focus on strategic financial decisions rather than data entry. Try Brex for free today.