Best Accounting Software for Shopify

The eCommerce businesses need to optimize their online store in such a way that they are able to sell more products and deliver excellent customer experiences.

For an eCommerce business to run successfully, it needs to have tightly integrated business management systems in place. 

For instance, an accurate and efficient inventory management solution integrated with the online store can help the seller in managing inventory and avoiding out-of-stock situations.

Likewise, an online seller is in need of easy-to-access updates on the state of his business. An accounting solution integrated with the online store automatically updates accounting data as and when the purchase orders are generated, payments are released, and inventory is moved.

The accounting software generates up-to-date reports that help a business understand its cash flows and balance sheets. Further, such reports also help the business owners to manage sales and inventory and be prepared to file taxes.

Thus, it’s important for eCommerce sellers to have an accounting solution in place that integrates with their online store and captures data as and when it gets updated.

Many online businesses create their online stores on Shopify. It is a powerful tool that helps them drive sales and manage day-to-day operations. Shopify when integrated with accounting software helps sellers in syncing their customer data and automating the entire order processing. 

In fact, Shopify’s integration with an accounting solution helps a business generate invoices and automatically process payments.

But the question that many retailers and resellers have is which is the best accounting software for Shopify? Well, in this article, we are going to reveal our top five preferences for the best accounting software for Shopify.

But before we reveal the list, here are some of the factors that you should consider before choosing accounting software for Shopify.

Things To Consider Before Choosing Shopify Accounting Software

The following are the criteria in relation to choosing appropriate accounting software for Shopify. 

1. Features

The first and foremost criteria that sellers must consider is to understand the features that an accounting software offers. In addition to this, they also need to ensure that such a solution aligns with their Shopify online store.

Thus, sellers must evaluate the features they would want at present, features they will want in the future, and the features they will use frequently before investing in any accounting software.

When evaluating a Shopify bookkeeping solution, eCommerce sellers must ensure that it is scalable and grows with their Shopify online store.

2. Fit

This is the second important criterion that an online retailer must look for when choosing the Shopify accounting app. He needs to determine how well the accounting solution integrates with Shopify and its underlying technology.

3. Installation

Installation and integration of accounting software may involve certain hurdles, just like any other software integration. To ensure satisfaction and compatibility, the seller must always use the Shopify bookkeeping app for a trial period.

4. Customisation

Another important consideration is the accounting solution’s flexibility. However, the costs involved in specific customization can often be very high and outweigh the benefits. How open or willing the seller is to make these custom changes to the accounting software that integrates with Shopify should also be taken into account.

5. Integration

When reviewing Shopify accounting software, a seller should consider integrated suites. How these align with his IT strategy is important as this will prevent an entangled complex application landscape. Thus, to avoid such a thing, the sellers need to consult all software users in their organization when deciding which to implement.

6. Import and Export of Information

A seller ensures that the Shopify accounting software can easily import or export data from the Shopify online store as and when it gets updated. Thus, a seller must consider the ease of transferring information as one of the factors in deciding on the Best Accounting Software to sync with Shopify. 

7. Access and Related Controls

The use of mobile devices has increased dramatically and is one of the most anticipated challenges that sellers expect to come across. Thus, many online sellers and retailers will want to make use of Shopify accounting software that is not connected to the office network at all times. 

Note that the ability to work off-site or remotely has become a basic requirement. This may involve additional applications or integrations, which in turn have cost implications and come with control challenges.

It is important that the Shopify accounting app incorporates controls to manage database changes. This is to ensure that no data is lost and that version control is securely maintained. 

Cloud computing has made it easier to work remotely as online sellers or retailers are able to log in with only a password, anytime, anywhere. Again it is important that the Shopify bookkeeping app has sophisticated access control. This is to ensure that only authorized personnel are allowed to make certain changes. 

8. Training 

Training is important when implementing accounting software that integrates with Shopify. Thus, the online sellers or retailers must ensure that they get the requisite training on using the Shopify accounting app. The seller must take into account the cost around training into account when considering different Shopify accounting software options. This would include consulting time, assistance with installation, data conversion, and sufficient training for all staff.

9. Support 

Ongoing support and timing of support is another important factor that online sellers and retailers must consider before selecting the best accounting software to sync with Shopify. This would include on-site services or support, online help and knowledge base, and adequate telephone support with an acceptable response time. 

The seller must consider all this when entering or negotiating the terms of a response service level agreement (SLA) with the Shopify accounting software provider. In addition to this, the seller must also determine the cost of support and the turnaround time regarding “bug” fixes.

10. Cost 

Cost is one of the most important considerations when choosing an accounting software that integrates with Shopify. Thus, the seller should identify what determines the price, per-user, or per-license. 

To estimate the price of a license, a seller can begin with what he can afford. It is however important to consider if the product is scalable to accommodate growth. Note that the best Shopify accounting software is the one that pays off by increasing the online seller’s or retailer’s profitability.

Best Accounting Software for Shopify

The following is the list of the top 5 best accounting software for Shopify.

1. QuickBooks Online

QuickBooks Connector Application
CostFree Version: $0
QBO Essentials: $25/month
QBO Plus: $40/month
QBO Advanced: $90/month
WebsiteShopify App Store, QuickBooks App Store
After-Sales SupportHoursMon – Fri, 5 am – 6 pm PSTFor Sales: 1.877.683.3280

QuickBooks Connector by Intuit helps an online seller connect his Shopify store and QuickBooks Online Accounting to automate bookkeeping and accounting tasks. Online sellers will never have to manually enter invoices, customers, or products again once their Shopify store is integrated with QuickBooks Connector.

In fact, online sellers can connect all of their Shopify storefronts to QuickBooks Online accounting to track income and expenses. Thus, accurate tracking of income and expenses will help them maximize their tax deductions.

Also, the online sellers need not update stock levels manually between QuickBooks Online and Shopify. That’s because the QuickBooks Connector synchronizes the online seller’s inventory and accounting data between Shopify and QuickBooks Online.

Also, tasks like entering invoices, customers, or products get automated when Shopify is connected with QuickBooks Online. 


  • Automatic import of Shopify sales, order details, and inventory into QuickBooks. All orders and refunds of online sellers from Shopify show up as sales receipts in QuickBooks. Each order that the seller exports from Shopify into QuickBooks automatically includes all items and taxes including shipping.
  • Complete Summary of Orders and their Total Value. Also, they can see a breakdown of their products and their profit margins.
  • Business On The Go. Sellers can create invoices and see their company’s activities anytime, anywhere.
  • Automation Of Spending and Bill Management. Online sellers can set up recurring payments for automatic bill pay that is quite effortless.
  • Connect Bank and Credit Card Accounts. Retailers and online sellers link their bank and credit cards for automatic downloads and categorization.
  • View Key Business Financials in a Single Dashboard. Online sellers can view their income, expenses, outstanding invoices, and other business financials in a simple and easy-to-understand dashboard. They can also generate profit & loss, balance sheets, and dozens of other reports with a single click. 

Besides using the QuickBooks Connector by Intuit app, online sellers can also use Quickbooks Sync by Wegibility application. 

This application connects QuickBooks Online with Shopify and automates bookkeeping for online sellers. It brings online sellers’ entire data and systems are combined together in one dashboard. 

Online sellers do not have to manually update daily tasks as they get updated automatically across all the seller’s channels. Also, the online seller’s bookkeeping and accounting are up to date at all times which means they are always on top of their cash flow. 

Quickbooks Sync by Wegibility helps the online seller’s team to spend less time on clerical work and moving between multiple applications. That is, the cloud-based eCommerce automation application leverages data across the seller’s systems. As a result, it gives online sellers insights into their business performance and profits.

Quickbooks Sync by Wegibility Application
CostPro Version: $49/month
WebsiteShopify App Store, Webgility Store
After-Sales Supportsupport@webgility.com, (877) 563-3037


  • Avoid Manual Bookkeeping. The orders, customers, sales tax, and fees of online sellers selling products on Shopify are securely and automatically recorded into their QuickBooks Online software. This means manual data entry, CSV files, and spreadsheets get eliminated.
  • Up-to-Date Financials. The online seller’s income is recorded with each transaction or each payout in real-time. That is, as and when the sales are made on the seller’s Shopify store. This means that the online seller’s books are always current and accurate.
  • Reconcile Books with Ease. Sellers can manage online orders on Shopify store individually or in batches and then easily post back to QuickBooks. This means that the seller’s bank always matches with his books.
  • Sync Data Seamlessly. Online sellers can ensure the accuracy of orders, fees, deposits, and inventory with seamless syncing from their Shopify store to QuickBooks. They can manage Shopify accounting and bookkeeping from a single dashboard with all the tools that online sellers need to scale.
  • Reduce Errors. Quickbooks Sync by Webgility application automates accounting. This means the software securely captures data from Shopify and other channels and posts it directly to QuickBooks on the online seller’s schedule. 

What does the Quickbooks Sync by Wegibility and Shopify Integration Do?

  • Post orders to QuickBooks as sales receipts, sales orders, invoices, or estimates
  • Consolidate orders and post them to QuickBooks as one transaction
  • Create purchase orders in QuickBooks
  • Changes made to order status in Quickbooks Sync Desktop are updated in Shopify 
  • Map payment methods and card types with QuickBooks (manually)
  • Download products from Shopify store to Quickbooks Sync Desktop
  • Sync product price and quantity between the Shopify and QuickBooks
  • Transfer (create) simple products from Shopify to QuickBooks or vice-versa
  • Transfer (create) variant products from QuickBooks to Shopify
  • Export list of QuickBooks and store products as CSV file
  • Bulk delete product mapping
  • Download customers from QuickBooks and Shopify store
  • Transfer customers from QuickBooks to Shopify and vice-versa

What the Quickbooks Sync by Wegibility and Shopify Integration Does Not Do?

  • Changes made to order status in-store are updated in Webgility Desktop
  • Generate marketplace sales report showing revenue, expenses, fees, and net income of each order
  • Process offline payments
  • Download customer groups from Shopify store

2. Xero

Xero Accounting Application (A2X)
CostEarly Version: $12/month
Growing Version: $34/month
Premium 5 Version:  $65/month
After-Sales SupportSupport

Xero is online accounting software that integrates with the seller’s online Shopify store seamlessly. The cloud accounting software has all the tools that online sellers need to run their business online.

Xero combines Shopify’s sales tools with its powerful accounting functionality so that online sellers have a better view of their business performance and are able to undertake easier eCommerce.


  • Shopify sales transactions flow automatically from Shopify to Xero. This means sellers can reconcile sales transactions against their bank data in just a few clicks. Thus, there is no need for online sellers to maintain spreadsheets as their Shopify accounting and bookkeeping gets simplified.
  • Online sellers can track their business performance in the Xero dashboard. Also, the sellers can use Xero’s cash flow and insights tools for an in-depth look at their business performance and hence make informed decisions.
  • Sellers get access to more accurate data. There is no need for them to manually export their Shopify data for finance purposes. That’s because Xero will automatically show their Shopify sales on a daily basis. The online accounting software will also give a breakdown of costs thereby enabling the online sellers to see how much profit they’ve made.
  • Online sellers do not have to worry about data security. Xero provides multiple layers of protection for the personal and financial information the sellers entrust to Xero. 
  • They can keep a count of the items available in stock. Sellers can run inventory management reports to find out how well different items are selling. In fact, they can even adjust the quantity on hand, the average cost, or the total value of a tracked inventory item.
  • Create and send customized purchase orders online with purchase order software. Online sellers can even convert POs into bills for payment, or into invoices to recoup costs. They can track which orders have been sent, which have been filled and billed by the supplier, and which are unfilled. 

What the Xero and Shopify Integration Do?

  • Syncs online seller’s Shopify sales transactions to Xero automatically.
  • Enables the online seller to control the payment gateways for which the seller’s invoices are generated as per his needs.
  • Creates a daily summary invoice per payment gateway, without having to enter data manually.
  • Clearly breaks down invoices into sales, discounts, shipping, refunds, gift cards, fees for Shopify payments or PayPal payments.
  • Provides the online seller with the option to have the invoices paid into a clearing account while awaiting payment from Shopify Payments or PayPal.
  • Enables the online seller to add bank account details for reconciliation of Shopify payments and PayPal.

What the Xero and Shopify Integration Does Not Do?

  • Xero and Shopify integration does not include inventory, COGS, split sales, import customer details, or individual Shopify orders.
  • The integration only gives a simple view of daily sales in the form of importing a simple summarized invoice. 
  • The online seller will have to integrate more applications with Xero for specialized tasks.

3. Sage Shopify Integration (A2X)

Sage Accounting Application (A2X)
CostStart Version: £12/Month
Standard Version: £24/month
Plus Version:  £30/month
WebsiteSage Accounting, A2X Accounting
After-Sales Support0191 479 5988

One of the other best accounting software for Shopify is Sage accounting. Sage Accounting is online accounting software that makes it easy for online sellers to run their businesses. It allows business owners to collaborate with their team members in real-time and get up-to-date accounting data from them.

Moreover, the online sellers can sync payments automatically with Sage Accounting. In addition to this, they can set up recurring invoices and pull in additional data from bank feeds in Accounting.

The online sellers also get an automatic posting of salary journals into Sage Accounting and a complete view of their business. They get paid on time and are able to protect their cash flow with personalized invoices that they can easily track. 

Sage Accounting solution offers an intuitive dashboard that displays a complete picture of money coming in and going out of the seller’s business each month.

Note that online sellers having a store on Shopify can easily undertake Sage Shopify eCommerce integration. For integrating Shopify with Sage accounting, all a seller needs to do is set up sync parameters with preconfigured settings in the cloud. Then, a seller needs to add Shopify API keys and start syncing price, stock & product data.


  • Sync orders, price, and inventory. Sage Shopify syncs the seller’s critical information to and from Shopify, making running an online store admin free. This means that  Sage Shopify is notified whenever an order is placed on the online seller’s sales channel. Once the order gets raised in Sage Shopify, consequently it gets raised in Sage Business Cloud. The seller can determine what order type or document type is raised in Sage Business Cloud based on the payment method type.
  • Take benefit of Shopify Plugins. Online sellers can take complete benefit of all the Shopify plugins. These plugins will help the Shopify sellers in increasing sales, get access to design templates, and get the ease of setup. This means there is no need for the seller to move to a new platform.
  • Track Inventory. Online sellers selling on Shopify can get access to real-time stock data. They can even set the minimum to reorder levels and can access easy-to-understand inventory reports. In addition to this, the online sellers also get alerts for products going out of stock. This helps them in staying on top of their inventory and save valuable time.  
  • Control Finances. Online sellers can connect their banks to Sage Accounting and import transactions automatically. This helps them in getting an accurate, real-time view of their accounts. That is, the online sellers have a clear picture of money going in and out of their business.
  • Trade in Multiple Currencies. In case the sellers have customers and suppliers abroad, Sage Accounting gives them the flexibility to create invoices in multiple currencies. Besides this, they can even accept payments, import bank transactions, and track expenses in multiple currencies to grow their business internationally. Note that this feature is available with Sage Accounting Plus. 

It is important to note that A2X posts a seller’s Shopify sales and fees directly into Sage. It is done in the form of clean summaries that match the payments to the seller’s bank account. Think of A2X as a financial housekeeper that sits between a seller’s Shopify store and his Sage accounting system. As a housekeeper, A2X cleanses, sorts, and summarizes a Shopify seller’s transactions while he gets on with his business.

What the Sage Accounting and Shopify Integration Do?

  • Generates summarised journal entries showcasing the breakdown of Shopify seller’s bank deposits without blocking his Sage accounting system. 
  • Access to Chart of Accounts created using the accrual method of accounting. This allows the online sellers’ cash flow to span over months. As a result, a seller gets a true and fair view of his online business and is able to make informed financial decisions. 
  • Payouts matched for the seller so that reconciliation consists of confirming these matches with the seller’s Sage accounting software. 
  • Accounts and taxes are mapped automatically every time once the seller maps it initially. 
  • Access to accurate accounts. This ensures that the risk of human error from manual calculations gets eliminated.

What the Sage Accounting and Shopify Integration Does Not Do?

  • Cataloging/Categorization
  • Channel Management
  • Email Marketing
  • Inventory Tracking
  • Marketplace Integration
  • Multi-Channel Marketing
  • Order Management
  • Promotions Management
  • Returns Management
  • SEO Management
  • Shipping Management
  • Shopping Cart

4. Freshbooks Shopify Integration

Sage Accounting Application
CostFree Version: $0
QBO Essentials: $25/month
QBO Plus: $40/month
QBO Advanced: $90/month
WebsiteShopify App Store, QuickBooks App Store
After-Sales SupportHoursMon – Fri, 5 am – 6 pm PSTFor Sales: 1.877.683.3280

The fourth on our list of Shopify accounting software is FreshBooks. FreshBooks is online accounting software that makes running a business easy, fast and secure. It makes accounting and bookkeeping tasks a breeze which means that sellers have to spend less time on accounting.

It is simple and intuitive to use accounting software packed with powerful features like invoicing, organizing expenses, tracking time, and following up with clients in just a few clicks.

FreshBooks automates a number of accounting tasks for eCommerce sellers so they can spend more time driving traffic to their online store. For instance, online retailers can generate invoices automatically. Likewise, they can track expenses and record payments automatically.


  • Create Professional Invoices. With FreshBooks, online sellers can create professional-looking invoices very easily. It’s simple to create and customize invoices with FreshBooks’ invoice generator. 
  • Track Business Expenses. Online sellers can connect their bank account or credit card to FreshBooks to automate data entry. Each day the seller’s FreshBooks account is updated with his most recent spending. This means that the seller’s business is always up-to-date automatically.
  • Accurate Reporting. FreshBooks Double-Entry Accounting identifies revenue items and their related expenses. Thus, it ensures that the online seller has an accurate calculation of profits and losses. Furthermore, FreshBooks automatically checks the transactional data and ensures that the debit and credit amounts are balanced out. This reduces the chance of errors greatly and helps online sellers file taxes.
  • Automated Bank Reconciliation. FreshBooks Bank Reconciliation feature helps online sellers organize their transactions easily. This feature imports and categorizes financial transactions automatically. Further, it makes changes and additions to reconcile banks with books of accounts or approves the automated matching suggestions.
  • Generates Financial Reports. FreshBooks’ insightful dashboards and reports give online sellers valuable information regarding their business performance. Sellers can easily access important reports like profit and loss and avoid manual calculations. Thus, sellers can save on time and make tax season stress-free.

What do the FreshBooks and Shopify Integration do?

  • Sync customers, products, and services manually or automatically.
  • Merge customer, product, and service information in real-time across platforms to simplify billing with consolidated customer invoices.
  • Automatically sync vendor information on each invoice, ensuring and improving accuracy with full product or services information.
  • Automatically sync each customer’s product or service, quantity, description, billing cycle, and taxes; allowing sellers to provide a more personalized experience and manage data more effectively.
  • Generating customized reports and 360-degree views of each customer’s profile and real-time actions.
  • Automating line of business applications to foster seamless connections with multiple databases and internal management systems.
  • Delivering customer-centric tools for order fulfillment, support requests, and ticketing applications.

5. Zoho Books

Zoho Books Accounting Application
CostFree Version: $0
Standard Version: $15/month
Professional Version: $40/month
Premium Version: $60/month
WebsiteZoho Books
After-Sales SupportUS – 8443165544UK – 08000856099Australia – 1800911076South Africa – 27214268110Canada – 15146736167support.usa@zohobooks.com 

Zoho Books is online accounting software that helps online sellers manage their finances, automate business workflows, and help them work collectively across departments. It handles all the tedious accounting tasks for online sellers including raising sales orders, invoicing, bookkeeping, etc. This enables them to focus on driving traffic to their Shopify store and convert traffic into leads.

In addition to this, it helps online sellers know their sales tax liability and prepare audit reports in accordance with IRS guidelines. Online sellers can add more of Zoho’s 40+ apps to help them manage and run their online business from wherever they are.

In addition to this, online sellers can maintain a clear record of the tax payments they have made. They can record their tax dues and reconcile the transactions within Zoho accounting software.

Online sellers can even see a summary of the sales tax that they have collected and the payments they have made to their vendors. Zoho Books provides online sellers with consolidated reports that are ready to be exported and filed at tax time.


  • Manage Receivables. With Zoho Books, online sellers can create professional-looking invoices within seconds. They can track payments easily with payment reminders. In fact, online sellers can get paid faster by giving their customers the online payment option. Zoho Books also offers the multi-currency pricing feature to help sellers grow beyond borders. Also, with ZohoBooks, sellers can create recurring invoices for their regular customers and set up credit cards so they can pay securely. Additionally, sellers can manage refunds and returns with credit notes.
  • Manage Payables. Online sellers can create and send purchase orders with ZohoBooks and stay on top of their payables. That is, they are aware of where their money is going with ZohoBooks. Sellers can create an open bill for the purchases they have made and see Zoho Books adjusting their stock level on receipt of goods automatically. Also, they can create recurring bills for purchases made at regular intervals, and allow Zoho Books to send them on their behalf.
  • Track Inventory. With Zoho Books, the sellers can keep complete track of inventory right from monitoring the stock levels to replenishing them. Tracking stock items means keeping an eye on stock levels at all times and overcoming the risk of stockouts. Plus, sellers can even set reorder levels and get alerts before the stock level falls below the minimum level. Additionally, the sellers can organize their inventory with information like SKU, product image, vendor details, cost, and stock on hand. Online sellers can also access detailed inventory reports to know the stock in hand and its valuation.
  • Bank Reconciliation. With Zoho Books, the sellers can securely fetch transactions from their PayPal and bank accounts. As a result, they can reconcile their accounts with bank statements effortlessly. Sellers can make use of bank rules to filter and categorize transactions automatically so that they do not miss categorizing any transaction.

What do the Zoho and Shopify Integration do?

Online sellers can use Zoho Flow to integrate Shopify with Zoho Books. As a result, they can automate many tasks that keep them away from focusing on their core operations.

  • Update the quantity and other details of a product or inventory item
  • Create orders and new discount codes
  • Add new products and create variants of an existing product
  • Create a new customer and update the details of an existing customer
  • Fetch:
    • the details of an existing order by ID, 
    • a product variant by title, 
    • the details of an existing order by name
    • the details of an existing checkout using token
    • a product by title
    • the details of the latest customer order by customer ID
    • the details of an existing discount code by code
    • an existing product variant by SKU
    • details of an existing customer by name or email address
  • Record payment for an existing customer invoice
  • Create a new invoice, new customer, new recurring invoice, new recurring expense, new recurring bill, new purchase order, new vendor, new credit note, etc.
  • Adjust and manage inventory

What the Zoho Books and Shopify Integration Does Not Do?

  • It does not offer many connections outside the Zoho ecosystem.

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