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    Best Accounting Software For Shopify Integration

    Last Updated | January 16, 2024

    An Overview: Top Accounting Software For Shopify Integration

    Shopify is one of the most popular eCommerce platforms that has managed to attract countless customers globally. Many businesses struggle in creating the best website for their store, in such a case you must consider hiring Shopify page design experts. Similarly, you can consider opting for accounting software for managing your store’s account.

    Since Shopify is an eCommerce platform, it involves money and accounting. To ensure that there are no errors in the accounting of your business, it is recommended that you rely on accounting software for your Shopify store. Even if you are considering migrating to Shopify from another platform, you must know that you will require accounting software. Get in touch with the best shopify migration agency.

    Shopify integration

    You must be thinking isn’t it a better idea to do your accounts manually? Well, you can; there is no harm in it, but it increases the chances of errors and is also a time-consuming task. We live in this digital era, where almost all business-related tasks have been automated to a greater extent.

    So, to help you choose the right accounting software for your Shopify store, we have narrowed down the list for you and have discussed the five best accounting software for you.

    Continue reading to find the best accounting software for Shopify integration.

    How Does Shopify create Financial Statements

    How Does Shopify create financial statements


     How Can You Do Accounting On Shopify?

    Having a store on Shopify is just one part of your business. Designing the perfect store might be a daunting task for some, therefore, you should consider a Shopify web development agency to help you with it. Another option could be to hire Shopify app developers for design.

    The sales you make, the profits, assets, etc. all have to be monitored. Keeping a track of your incoming and outgoing cash is important to help in the running of your eCommerce business.

    Shopify does offer its users a basic default report regarding their business. However, this report is very basic and might be sufficient for a newly established business. In addition to this report, small businesses might even have to maintain one or two spreadsheets to keep a track of all their transactions.

    Once your business starts doing well and you start dealing with six figures, you might want to explore accounting software as dealing with too many numbers can be overwhelming for you. For this reason, Shopify allows users to integrate accounting software with their stores to manage their accounting very smoothly.

    There are many accounting software available in the market that you can use to integrate into your store. The five best accounting software have been discussed in detail in this post. These integrations are:

    –Shopify FreshBooks

    Shopify NetSuite

    Shopify QuickBooks

    Shopify Xero

    Shopify SAP Business

    I hope this table format helps make the steps clearer for you:

    This table format helps make the steps clearer for you:

    Step Description
    1. Set Up Your Shopify Store
      – Sign up for a Shopify account and create your online store.
      – Configure your store settings, including currency, taxes, and payment gateways.
    2. Choose an Accounting Method
      – Decide whether you want to use the cash or accrual accounting method. Consult with an accountant to determine which method is best for your business.
    3. Integrate Accounting Software
      – Shopify integrates with various accounting software solutions like QuickBooks, Xero, and Wave. Connect your Shopify store to your chosen accounting software.
    4. Sync Your Transactions
      – Once integrated, your transactions will automatically sync to your accounting software. This includes sales, refunds, shipping fees, and taxes.
    5. Categorize Transactions
      – Review and categorize your transactions to ensure they are accurately recorded. This includes categorizing income, expenses, and fees.
    6. Reconcile Bank Statements
      – Regularly reconcile your bank or payment processor statements with your accounting records to ensure accuracy.
    7. Manage Inventory
      – Keep track of your inventory levels using Shopify’s built-in inventory management or a third-party app for inventory management. This is crucial for accurate cost of goods sold (COGS) calculations.
    8. Track Expenses
      – Record all business expenses, including advertising costs, shipping fees, and any other expenses related to your Shopify store.
    9. Handle Taxes
      – Set up tax rates and ensure that taxes are calculated correctly for your products and customers’ locations. Your accounting software should help with tax reporting.
    10. Generate Financial Reports
      – Regularly generate financial reports such as income statements (profit and loss), balance sheets, and cash flow statements to analyze your business’s financial performance.
    11. Payroll and Employee Management (if applicable)
      – If you have employees, consider integrating a payroll system with your accounting software to handle payroll processing and tax withholdings.
    12. Regular Reconciliation
      – Perform regular reconciliations to ensure that your Shopify sales data matches your accounting records.
    13. Consult with an Accountant
      – It’s advisable to consult with an accountant or financial advisor who is familiar with e-commerce businesses to ensure compliance and accurate financial reporting.
    14. Plan for Taxes
      – Prepare for tax season by setting aside funds for income taxes and filing all necessary tax documents on time.
    15. Audit and Review
      – Periodically audit your financial records to catch any discrepancies or errors and make adjustments as necessary.
    16. Backup and Security
      – Keep backups of your financial records and ensure that your accounting software and Shopify store have strong security measures in place to protect sensitive financial data.


    Shopify FreshBooks Integration

    FreshBooks is a cloud accounting software that is available as a web and mobile app (Android, iOS). This software is most popular amongst small businesses but can be helpful for larger businesses too, as it lets the user split expenses for their projects. With FreshBooks, you can manage your taxes reducing the time you spend in preparing and filing taxes.

    FreshBooks offers various price plans to its users, ensuring that all businesses are catered to.

    These price plans are:


    Starts at $15 per month. This is good for any business that just requires basic features.


    Shopify Plus store Starts at $25 per month. This is good for businesses that want more features and automation. This is the most popular price plan.


    Starts at $50 per month. This price plan is well-suited for businesses that want to expand and want to give their employees more control of the business.


    This price plan is custom-made and is good for those businesses that have more complex needs.

    Before you sign up for a price plan, you can avail of a 30-day free trial.

    Why is FreshBooks good for me?

    –Get a desktop and mobile version to manage your accounts from anywhere

    –File taxes easily

    –Split expenses for your projects

    –Live customer support is available

    –Import financial data from various sources

    –Limit the access of employees to financial reports

    Read Also Top ERP for Shopify

    Integration With Shopify

    FreshBooks allows integration with Shopify, helping in simplifying and speeding up the process of bookkeeping. With the Shopify FreshBooks integration, details regarding all products, invoices, inventory, and payments are received from Shopify into FreshBooks.

    The integration takes place when you have a FreshBooks account and when you choose the option of syncing with your Shopify store. This integration allows you to either sync all the data manually or automatically. If you choose the automatic option, orders are synced every 15 minutes, and when you choose to sync the orders manually, you can sync them whenever you want. The total time required for this process is a maximum of 15 minutes.

    If you wish to choose a third-party app connector, you can rely on expert Shopify partners. There are many options available in the market to help you with this integration process.

    Read Also Shopify Stripe Integration

    Shopify NetSuite Integration

    NetSuite is best suited for large businesses as it is an Enterprise Resource Planning (ERP) system, making it the most expensive Shopify integration. With the hefty price tag comes several valuable features. It is estimated to cost $999 per month, but the cost depends on the features one wants. They also offer a free trial before you sign up for the ERP. NetSuite is also available on Android and iOS, in addition to the desktop version.

    Why is NetSuite good for me?

    –Get industry-specific features

    –Automate almost all business tasks

    –Better synchronicity among all the employees

    –Easy integration with Shopify

    Integration With Shopify

    There are many connector apps available on the Shopify App Store that can help you with the integration. If you wish to opt for professional services, you can do that too. Folio3 is a well-known software company that can provide you with Shopify expert help. The connector for NetSuite by Folio3 is known as the Shopify Connector- NetSuite Integration App.

    Shopify QuickBooks Integration

    QuickBooks is another cloud-based accounting software that is good for small and mid-sized stores. It offers various features to its users based on the price plan they sign up for.

    The price plans offered by QuickBooks are the following:

    –Simple Start

    Provides the user with basic bookkeeping tools from $25 per month.


    Provides an automated billing feature. Good for growing businesses. Starts from $50 per month.


    Get better organizing and managing features with this price plan at $80 per month.


    At $180 per month, get advanced features with a dedicated support system for your business.

    QuickBooks offers its users a 30-day free trial. In addition to the price plans discussed above, QuickBooks also offers their users a price plan for self-employed people, known as the Freelancer price plan at $15 per month.

    Why is QuickBooks good for me?

    –Simple user interface

    –Offers integrations with Shopify

    –Extensive accounting reports provided

    Shopify Integration

    For the Shopify QuickBooks integration, you can opt for any connector app available on the Shopify App Store or shopify app development services. This process is a quick one and leads to the smooth running of your Shopify store.

    Shopify Xero Integration

    Xero is a great option for businesses that are constantly on the go. This software is targeted toward small businesses that require constant updates even when they are on the go. This software can be synced with multiple devices at the same time to ensure you receive real-time data regarding your accounts.

    Xero offers the following price plans:


    This price plan is good for new businesses and even the self-employed. It starts at $12 per month.


    This is the most popular price plan and is good for growing small businesses. It starts at $34 per month.


    This price plan is recommended for all established businesses and requires the user to pay $65 per month.

    Why is Xero good for me?

    –Allows unlimited users

    –Get real-time bank updates and feeds

    –Get equity reports that show all investments and draws made

    –Track metrics and check your financial health with Analytics Plus

    Integration With Shopify

    For the Shopify Xero integration, you must have a Xero account, before you can sync these two. You can download the Shopify Xero integration app from the Xero app store, opt for a connector of your choice from the Shopify App Store, or even opt for professional services. After this integration, you can have a clearer picture of your Shopify store accounts.

    Shopify SAP Business ByDesign Integration

    SAP Business ByDesign is another ERP solution for your business. It is a great option for large-scale and well-established businesses, that helps in better cash flow management and CRM (Customer Relationship Management).

    Although SAP Business ByDesign is an ERP software, it is much more affordable than other ERP software, making it more affordable for smaller businesses as well. Small scale businesses, if they want to invest in ERP software to automate their business tasks, then this would be a great option.

    SAP Business ByDesign offers the following price plans:

    –Self-Service User

    Priced at $21 per user per month, it is a good option for businesses to help them in performing core self-service tasks.

    –Core User

    Priced at $117 per user per month, it helps in managing all the daily work activities related to accounts, planning, sales, and your employees.

    –Advanced User

    Priced at $212 per user per month, you can get access to all the features and functionality provided by SAP Business ByDesign.

    They even offer a free trial for all their price plans, which can be beneficial for you before you sign up for a price plan.

    Why is SAP Business ByDesign good for me?

    –Data security is never compromised

    –Keep your employees abreast with all the details regarding your business

    –Can even be used by small businesses

    Integration With Shopify with the best Shopify optimization agency

    You can integrate your Shopify store with SAP Business ByDesign by using any connector app or professional services.

    Final Thoughts About Best Accounting Software For Shopify Integration

    Shopify is an eCommerce platform that can integrate with almost every accounting software. If you are looking for solutions for your Shopify store, then you must consider working with Folio3. Their Shopify developer can provide you with all the solutions you need for your store.

    FAQs About Accounting Software For Shopify Integration:

    What accounting software is compatible with Shopify?

    Shopify is compatible with numerous accounting software available in the market. You just need to use a connector app as a bridge between the two platforms to help in the synchronization process.

    Does Shopify track accounting?

    Shopify provides its users with a very basic report for transactions. There are no in-depth reports on the accounting of your store. Therefore, you need to rely on other accounting software, especially if you have a higher number of sales going on.

    How do you categorize Shopify in QuickBooks?

    Once you have completed the Shopify integration, click on the Accounting tab on your QuickBooks dashboard select Chart of Accounts, and click on New. You can choose whichever category is best suited.



    Folio3, a Software Powerhouse established in 2005, is one of the leading eCommerce solution providers for SMBs and Fortune 500. The Company has expertise in diverse industries such as Animal Care, Retail, Automotive, Food and Agriculture, and Health care. From ecommerce store design and development to full-scale ERP deployment and integration, Folio3 has done it all.