Shopify Bookkeeping – 10 Best Accounting Software and Apps

In this digital era, traditional bookkeeping methods are making way for innovative solutions. In this blog, we will explore the concept of Shopify bookkeeping and why it matters to eCommerce entrepreneurs

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In the fast-paced world of eCommerce, managing your Shopify store’s finances is no small feat. From tracking sales to calculating taxes, efficient bookkeeping is essential for your business’s success. Welcome to our comprehensive guide on Shopify Bookkeeping: Accounting Apps, Best Practices, and Tips.

In this digital era, traditional bookkeeping methods are making way for innovative solutions. In this blog, we will explore the concept of Shopify bookkeeping and why it matters to eCommerce entrepreneurs. We’ll delve into the challenges unique to eCommerce bookkeeping and provide practical advice on best practices. Additionally, we’ll guide you through the process of selecting the right accounting app for your Shopify bookkeeper, ensuring your financial management is as seamless as possible.

What is shopify bookkeeping?

What is shopify bookkeeping

Shopify bookkeeping, indeed, refers to the process of tracking, recording, and managing financial transactions and records for businesses that operate on the Shopify platform. Consequently, it plays a crucial role in ensuring the financial health and success of your eCommerce venture.

At its core, it involves:

1. Sales Recording

Shopify’s accounting begins with meticulous tracking of all sales made through your online store. This includes recording customer orders, payment methods, and order details for accurate financial records.

2. Expense Tracking

Efficient expense tracking is essential to monitor and control your business costs effectively. This encompasses recording all expenditures, such as product costs, shipping fees, and marketing expenses.

3. Tax Management

Managing taxes is crucial. Calculate and set aside the appropriate amount of taxes based on your location and where you sell your products.

4. Financial Reporting

Generate regular reports to gain insights into your business’s financial health, including revenue, profit margins, and cash flow.

5. Reconciliation

Ensure your Shopify records align with bank statements and other financial documents to maintain accuracy and financial integrity.

Accurate Shopify bookkeeping is vital for several reasons

1. Compliance

Shopify’s accounting ensures your business meets tax and legal requirements by accurately tracking transactions and taxes.

2. Financial Planning

It provides essential data for informed decisions, helping you allocate resources effectively and plan for growth.

3. Profitability

With precise records, you can gauge your business’s financial health, optimize pricing, and identify areas to boost profits.

Consider using specialized accounting for shopify software or hiring a expert to streamline this process and ensure your financial records are in order. Proper bookkeeping is a cornerstone of successful eCommerce businesses on Shopify.

10 Best Shopify Accounting Software and Apps

10 Best Shopify Accounting Software and Apps

In the dynamic world of eCommerce, managing your Shopify store’s finances efficiently is crucial for success. Fortunately, a multitude of accounting software and  Shopify Bookkeeping are available to simplify this task. To help you make an informed choice, here are the top 10 Shopify accounting solutions worth considering-

1. QuickBooks Online

A widely-used cloud accounting software that seamlessly integrates with Shopify, providing real-time financial insights.

2. Xero

Known for its user-friendly interface and robust features, Xero can help streamline your Shopify store’s accounting processes.

3. Wave Financial

Ideal for small businesses, Wave offers free accounting software with essential tools for Shopify store owners.

4. Avalara

Automate sales tax calculations and compliance, ensuring your Shopify store stays tax-efficient.

5. ZapERP

An inventory management and accounting software that synchronizes seamlessly with Shopify, simplifying order and inventory tracking.

6. Sufio

Generate professional invoices for your Shopify store and effortlessly handle tax compliance for international sales.

7. QuickBooks Commerce

This inventory and order management platform integrates smoothly with Shopify, helping you maintain control over stock levels.

8. TaxJar

Automate your sales tax calculations, reporting, and filing, saving time and reducing compliance errors.

9. AccountEdge

A desktop-based accounting solution that offers advanced features for Shopify merchants seeking more control.

10. Quaderno

 Simplify your tax compliance with Quaderno’s automated tax calculations, invoices, and receipts for Shopify.

Choose the accounting software or app that aligns best with your Shopify store’s needs and watch your financial management become more efficient and effective than ever before.

How to Do Bookkeeping For Shopify

How to Do Bookkeeping For Shopify

Effective bookkeeping is crucial for Shopify store owners to maintain financial clarity and make informed decisions. Here’s a simple guide to get started:

1. Organize Your Finances

Proper organization is the foundation of effective Shopify bookkeeping. Start by categorizing income and expenses. Segment expenses into logical categories like advertising, product costs, shipping, and fees. This structure simplifies tracking and analysis.

2. Choose the Right Tools

Shopify integrates seamlessly with popular accounting software like QuickBooks and Xero. These tools automate data entry, reducing manual errors, and offer advanced reporting features. Select the one that suits your business needs to streamline bookkeeping processes.

3. Regular Reconciliation

Regularly reconcile your Shopify records with your bank statements. This practice ensures that your records match actual financial transactions. Reconciliation helps uncover discrepancies and maintain data accuracy.

4. Track Inventory

For businesses selling physical products, tracking inventory is vital. Keep a close eye on stock levels to avoid overstocking or running out of popular items. Accurate inventory management prevents revenue loss and customer dissatisfaction.

5. Monitor Tax Obligations

Understand your tax obligations as an eCommerce business. Stay informed about sales tax rules in your region and collect taxes where required. Compliance with tax regulations is essential to avoid legal issues.

6. Monthly Reports

Generate monthly financial reports, including profit and loss statements, balance sheets, and cash flow statements. These reports provide insights into your business’s financial health, helping you make informed decisions and identify areas for improvement.

7. Seek Professional Help

If managing bookkeeping becomes overwhelming, consider hiring an accountant or  Shopify bookkeeper experienced in eCommerce. They can offer expert advice, ensure compliance, and free up your time to focus on growing your Shopify business.

By following these steps, you’ll not only stay compliant with tax laws but also gain valuable insights to grow your Shopify business successfully.

9 Shopify Bookkeeping Best Practices

9 Shopify Bookkeeping Best Practices

Effective bookkeeping is essential for the success of your Shopify store. Additionally, here are nine best practices to help you manage your finances efficiently:

1. Dedicated Business Account

Open a separate bank account exclusively for your Shopify business. This separation of personal and business funds simplifies tracking and maintains financial clarity.

2. Regular Reconciliation

Monthly reconciliation is a must. Compare your Shopify transactions with your bank statements to identify any discrepancies, ensuring your records remain accurate.

3. Accurate Product Cost Tracking

Precise tracking of the cost of each product is vital. This allows you to calculate profits accurately and determine which products are most profitable.

4. Expense Tracking

Keep meticulous records of all business expenses, including shipping, advertising, software subscriptions, and any other costs associated with running your Shopify store.

5. Tax Compliance

Understand your tax obligations based on your location and the jurisdictions where you sell your products. Ensure that your store collects and remits taxes correctly for each sale.

6. Cloud Accounting Software

 Invest in a reputable cloud-based accounting for shopify software that integrates seamlessly with Shopify. This enables real-time tracking of your financial data and provides valuable insights for decision-making.

7. Organized Documentation

Maintain a well-organized system for storing invoices, receipts, and other financial documents. A digital or physical filing system makes it easier to locate and reference important paperwork when needed.

8. Regular Reporting

Generate financial reports regularly to monitor your store’s performance. Key reports include profit and loss statements, balance sheets, and cash flow statements. These reports offer a snapshot of your financial health and help you identify areas for improvement.

9. Professional Help

Consider hiring a Shopify bookkeeping expert or accountant, especially if your business experiences growth or complexity. Professionals can navigate intricate financial tasks, provide strategic advice, and ensure your books are accurate and compliant.

By following these best practices, you’ll have a solid foundation for effective Bookkeeping on Shopify, which can lead to better financial management and business growth

Can You Do Accounting In Shopify bookkeeping?

Accounting In Shopify

Shopify, being a powerful eCommerce platform, offers several tools and features to help you effectively manage your store’s financial aspects. However, while it doesn’t provide full-fledged accounting capabilities, you can certainly perform essential accounting tasks for Shopify within the platform. Here’s what you can do-

1. Sales Tracking

This involves monitoring every sale made through your Shopify store, keeping records of order details, customer information, and payment methods. Accurate sales tracking ensures you have a clear view of your revenue and helps identify your top-selling products.

2. Tax Management

Calculating and managing taxes can be complex, but Shopify simplifies this task by automatically calculating taxes based on your location and the jurisdictions where you sell your products. It ensures compliance with tax regulations and minimizes the risk of errors.

3. Expense Tracking

Running an eCommerce business involves various expenses, such as product costs, shipping fees, advertising expenses, and more. Expense tracking in Shopify helps you keep tabs on these costs, ensuring you have an accurate picture of your expenditures and can make informed financial decisions.

4. Financial Reporting

Generating reports is a crucial aspect of accounting in Shopify. It provides insights into your business’s financial performance, including revenue, profit margins, and cash flow. These reports are invaluable for assessing the health of your eCommerce venture and making data-driven decisions.

However, when it comes to comprehensive accounting tasks like double-entry bookkeeping, payroll management, and complex financial analysis, you’ll likely need dedicated accounting software for Shopify or the expertise of a professional accountant. Additionally, many accounting and Shopify Bookkeeping apps integrate seamlessly with Shopify, allowing you to synchronize your financial data for a more robust accounting experience.

How Can I Double Check The Tax Rate Shopify Is Charging Me?

How Can I Double Check The Tax Rate

1. Access Your Shopify Admin

Log in to your Shopify account and go to your admin panel.

2. Settings

Click on “Settings” at the bottom left corner of your admin page.

3. Taxes

Under the “Settings” menu, select “Taxes.”

4. Review Your Tax Settings

In the Taxes section, you can review your tax settings, including tax rates, tax overrides, and tax exemptions. Ensure that the tax rates for your specific products and regions are correctly configured.

5. Test Orders

To be absolutely certain, consider placing a few test orders. You can do this by making a purchase on your own store. During the checkout process, verify that the tax rates applied match your expectations.

6. Consult a Tax Professional

If you have complex tax requirements or if you are unsure about the tax rates, it’s advisable to consult a tax professional who specializes in eCommerce. They can help you ensure compliance with local tax laws and provide guidance on configuring your Shopify tax settings accurately.

By following these steps and conducting thorough checks, you can ensure that Shopify is charging you the correct tax rates for your products and regions, helping you avoid potential tax-related issues in the future.

Why Is Accounting And Bookkeeping Important For eCommerce Businesses Using Shopify Bookkeeping?

Why is accounting and bookkeeping important for eCommerce businesses using Shopify

Accounting and bookkeeping are paramount for eCommerce businesses utilizing Shopify for several compelling reasons.

Firstly, compliance: Accurate financial records ensure that your business adheres to tax regulations and legal obligations. This safeguards you from potential penalties and disputes.

Secondly, financial clarity: Sound they provides a clear, real-time picture of your business’s financial health. You can track revenue, expenses, and profits, enabling data-driven decisions.

Thirdly, strategic planning: With comprehensive financial data, you can create effective strategies for growth. Whether it’s optimizing inventory, marketing spend, or expansion plans, having a solid financial foundation is essential.

Fourthly, investor and lender trust: If you seek funding or loans, meticulous accounting demonstrates your business’s stability and reliability, enhancing your credibility with potential investors or lenders.

In summary, accounting and bookkeeping are indispensable for eCommerce businesses on Shopify bookkeeper. They ensure compliance, empower informed decision-making, enable strategic growth, and build trust with stakeholders, ultimately contributing to your business’s long-term success.

What Cloud Accounting Software Works Best For Shopify Bookkeeping Businesses?

cloud accounting softwares for shopify bookkeeping Businesses

When it comes to choosing the best cloud accounting software for bookkeeping businesses, several options stand out:

1.QuickBooks Online

QuickBooks seamlessly integrates with Shopify, allowing you to track sales, expenses, and inventory. It offers comprehensive reporting and scalability as your business grows.

2. Xero

Xero is user-friendly and offers strong eCommerce integrations. It enables you to reconcile transactions, manage inventory, and handle multi-currency transactions.

3. Wave

If you’re looking for a free option, Wave is a solid choice. It provides basic accounting features, making it suitable for small Shopify businesses with limited budgets.

4. Zoho Books

Zoho Books offers inventory management, expense tracking, and customizable invoices. It also integrates well with Shopify to streamline shopify bookkeeping tasks.

5. FreshBooks

Known for its simplicity, FreshBooks is ideal for freelancers and small business owners. It offers time-tracking, invoicing, and expense management features.

Ultimately, the best choice depends on your specific needs and budget. Consider factors like the size of your business, the complexity of your Shopify operations, and your long-term growth plans when selecting the right cloud accounting software. Many of these options offer free trials, so you can explore them to see which one suits your bookkeeping for shopify bookkeeper needs best.

Factors To Consider When Choosing an Accounting Shopify Bookkeeping App

Factors to Consider When Choosing an Accounting App

When it comes to managing the financial aspects of your Shopify store, choosing the right accounting app can make a world of difference. The right app can streamline your bookkeeping for shopify processes, save you time, and ensure accuracy in your financial records. Here are some key factors to consider when selecting Shopify’s accounting-

1. Integration with Shopify

Ensure that the app seamlessly integrates with your Shopify store. It should be able to pull in all relevant sales, expense, and inventory data without manual input.

2. Ease of Use

Look for an app that is user-friendly and doesn’t require extensive training. You want to spend your time running your business, not trying to figure out complicated accounting software.

3. Features and Functionality

Assess the features offered by the app. Does it handle inventory management, tax calculations, and multiple currencies if needed? Choose an app that aligns with your specific business needs.

4. Reporting Capabilities

Robust reporting is crucial for tracking your financial performance. Check if the app provides customizable reports and insights into your business’s financial health.

5. Scalability

Consider your future growth. Will the app accommodate an increase in transactions and data volume as your business expands?

6. Security and Compliance

Ensure that the app adheres to security standards and compliances to protect your sensitive financial data.

7. Cost

Evaluate the pricing structure of the app. Some charge a monthly fee, while others operate on a transaction basis. Choose one that fits your budget and offers value for the services provided.

8. User Reviews and Ratings

Check user reviews and ratings on Shopify’s app store or other reputable platforms. This can provide insights into the app’s performance and user satisfaction.

9. Customer Support

Consider the level of customer support offered by the app’s provider. Reliable customer support can be a lifesaver when you encounter issues or have questions.

10. Trial Period

If available, take advantage of any free trial periods to test the app’s functionality and suitability for your business before committing.

By carefully assessing these factors, you can make an informed decision and select the accounting Shopify app that best suits your eCommerce needs, ultimately helping you manage your finances more effectively and efficiently.

Challenges Of eCommerce Bookkeeping

Challenges Of eCommerce Bookkeeping

Ecommerce businesses thrive in the digital age, but they also face unique bookkeeping challenges.

Firstly, the volume of transactions can be overwhelming. Numerous daily sales, refunds, and payment processor fees can make tracking finances a time-consuming task.

Secondly, inventory management can be complex. Ecommerce businesses often deal with a wide range of products, and keeping track of stock levels and associated costs can be tricky.

Thirdly, international sales introduce currency exchange and tax implications that require careful attention.

Lastly, many e-commerce platforms integrate with various payment gateways and Shopify Bookkeeping, creating a web of financial data that must be synchronized and reconciled accurately.

To overcome these challenges, consider implementing robust accounting software and seeking professional help. Effective bookkeeping ensures financial transparency, compliance, and better decision-making, helping your e-commerce venture thrive.


Shopify bookkeeping isn’t just about crunching numbers; it’s the lifeline of your eCommerce venture. In this blog, we’ve uncovered the fundamentals and why it’s crucial for your business’s financial health. We’ve shared nine best practices to streamline your bookkeeping for shopify processes, discussed the challenges you might encounter, and provided insights into verifying tax calculations.

Furthermore, we’ve explored the importance of robust accounting for eCommerce businesses on the Shopify platform. To make your journey even smoother, we’ve highlighted the best cloud accounting software options tailored to Shopify’s accounting needs and curated a list of the top Shopify accounting apps. Finally, we’ve outlined key factors to consider when selecting the ideal accounting app to propel your business forward.

Armed with this knowledge, you’re well-equipped to navigate the complexities of Shopify’s accounting, ensuring your financial records are accurate, compliant, and conducive to the growth of your eCommerce enterprise.

Know more >>>Importance of Professional Shopify Product Listing Services​


1. What is Shopify bookkeeping?

Shopify bookkeeping involves tracking sales, expenses, and inventory from your Shopify store to maintain accurate financial records. It helps in understanding your business’s financial health and ensures compliance with tax regulations.

2. Can I use Shopify for accounting?

While Shopify offers basic financial reporting, integrating it with dedicated accounting software like QuickBooks or Xero provides comprehensive accounting capabilities, ensuring detailed financial management and accurate tax preparation.

3. How do I give my bookkeeper access to Shopify?

To give your bookkeeper access to Shopify, go to Settings > Account > Account and Permissions. Add them as a staff member with appropriate permissions, ensuring they can access the financial data they need without compromising your store’s security.

4. How to do e commerce bookkeeping?

E-commerce bookkeeping involves tracking sales, managing expenses, recording inventory changes, and reconciling bank statements. Using specialized software and regularly reviewing financial reports ensures accurate records and financial health.

5. Best Accounting Software To Use With Shopify

The best accounting software for Shopify includes QuickBooks, Xero, and FreshBooks. These tools integrate seamlessly, offering robust features for tracking sales, managing expenses, and preparing financial reports, making bookkeeping efficient and accurate.

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In this digital era, traditional bookkeeping methods are making way for innovative solutions. In this blog, we will explore the concept of Shopify bookkeeping and why it matters to eCommerce entrepreneurs