12 Best Shopify Accounting Apps – [2024]

This app is one of the best accounting apps on Shopify, but it’s only for the German speaking audience who use Shopify. Therefore, if you don’t conduct business in German, then you need to think of another Shopify accounting app for your store.

This app has several functions that allows you to streamline the accounting of your store within minutes. It integrates Shopify with Lexoffice. When orders are made on your store, there is a corresponding customer and invoice created within your Lexoffice account.

If you need personalization with your invoices, that isn’t a problem. This app allows you to enhance documents with custom pre and posttexts. Therefore, your invoices can be made personal to your brand.

The app can also save you significant amounts of time. You can have the tax documents ready for tax attorney in the popular DATEV format.

German accounting Integration Highlights:

• Saves you time when completing work.
• Great for those who work in Germany.
• Connects with the popular Lexoffice account suite.
• Allows you to customize your invoices.

If you’re using QuickBooks Online, you can connect your Shopify data with your online account automatically. You can complete this automatically or manually. The app supports multicurrency sellers, so if you sell in more than one territory, then this is a great accounting app to use. This app will also support you selling in one currency but reporting in another currency on QuickBooks then the app can handle this so QuickBooks has the right data.

The QuickBooks Bridge app can also help those who have multiple stores but one reporting system. This allows you to have one QuickBooks online account but multiple stores to maximize online earning potential. However, you will need to have a subscription for the app on each store.

The updates and synchronization of the data takes place once a day automatically. Or you can manually update the data yourself. The update will include orders, customers and more and will take into account any prepaid or pay-later orders. Refunds and cancellations are also synced through the app.

The app can also help you sync information about products and customers. You can have a new customer for every customer you have online or you can have all customers listed under a dummy customer on your QuickBooks Online account. The choice is yours and depends on how you want to analyze results.

This app is useful for companies who operate in many nations including the United States, United Kingdom, Australia, New Zealand, India, South Africa and more.

This app does not work with the QuickBooks desktop or QuickBooks self-employed versions.

QuickBooks Bridge Highlights:

• Connects your Shopify store with your QuickBooks Online account.
• Plenty of options for managing your account.
• Can help with multiple stores, but one QuickBooks Online account.
• Lots of ways data can be synced that allows you to keep accurate records.

A large part of keeping your financial data accurate is data entry. This is a long, tiresome job that many small business owners just simply don’t do. And when some people do enter in the information there can be huge errors from typos and more. This app helps you to reduce both problems by doing the data entry automatically for you and reducing errors by syncing your online store with QuickBooks.

The app allows you to record orders individually or summarized by day, week or month. It can help to automatically update your inventory in QuickBooks with every sale and then create missing products within QuickBooks and can even work with bundles and more.

The app is very versatile and can handle refunds and cancellations easily. It can create memos against the original sales to make the transaction level accounting more accurate. Plus, the app can handle all sales tax compliance and can be used when there are single or multiple tax jurisdictions. The app can also integrate with Avalara for more advanced tax functionality.

The app will also record all Shopify related fees. These will appear as a separate bill transaction. Plus you can be sure of the accuracy of your inventory as all levels are updated with every sale and return. So you will know when you’ve got loads of stock for one item and running short of another. Items can also be listed with variations for more inventory control.

QuickBooks Desktop Sync Highlights:

• Can sync with QuickBooks for quick and easy accounting updates.
• Monitor all aspects of your financial operations.
• Works across tax jurisdictions.
• Can help with inventory.

This is one of the only apps that allows you to reconcile your account with either Xero or Quickbooks. Most other apps allow you to integrate your Shopify account with one of these accounting firms, but not both. That is what makes this app one of the best.

The app allows you to have sales automatically sent and stored in your accounting system. Allowing you to know that everything is being accounted for correctly. You don’t have to wait or spend hours entering data or checking results to ensure that you have the right numbers.

The app allows for all calculations of fees, refunds and adjustments, making financial management of your online business much easier. Some people state that they think the work of hours is condenses into a few minutes worth of work.

The app is great for eCommerce businesses, but it is also designed to be used by professional bookkeepers and accountants so they can help clients manage their financial arm of their business. When a new client is taken on, professional financial services can even look back over the past 12 months of the Shopify store. This can help those clients who are struggling to clean their books.

The app is perfect for stores of all sizes. It can be used within Shopify Plus as well as some of the smaller stores who only manage a few orders at a time.

A2X for QuickBooks and Xero Highlights:

• Work with both QuickBooks and Xero.
• Can access records that go back 12 months, so great for onboarding when a new accountant or bookkeeper is hired.
• Perfect for businesses of all sizes from those who have limited activity on their store to those with lots of traffic and sales.
• Can help cut down processing time from hours to minutes, allowing business owners to get on with their work.

This is a great app for keeping your financial data in check, accurate and up-to-date. Within just a couple of clicks you can export your Shopify orders to your Xero accounting software to enjoy excellent financial reporting that can help you make important business decisions. The data can be exported manually or you can take advantage of the daily automatic exports.

Every order that is exported from Shopify will include all line items, shipping and taxes. If there are any Shopify payments, refunds, discounts or fees these are recorded separately. If you aren’t using Shopify Payments, then these fees won’t be grouped together automatically.

You can also import customer information into your Xero account for better management of financial data. And there is integration for tax wherever you’re based in the world.

Xero Integration by Bold Highlights:

• Automatic and manual exportation of data into Xero.
• Easy to use.
• Can be adjusted to any tax system across the world.
• Customer data can also be exported.

Connect your Shopify account with your QuickBooks online account. This will save you money and time when you no longer have to manually complete the operation. You can also take advantage of several features in QuickBooks that can help you make more of your business with better decisions.

The app works by creating an invoice in QuickBooks Online every time that an order is placed. It will also create products, deposits and change stock levels automatically for you, so you can keep your financial information up-to-date and easily read by you, accounting teams and other experts.

You can also retrieve orders from Shopify within QuickBooks Online for more details. This can be done by selecting the corresponding Shopify order by status. You can also make QuickBooks Online assign invoice numbers instead of Shopify’s own invoice number generator.

The app can also assign sales to different customer groups. You can have original customers, organizations, generic customers and more. You can also assign sales to class and locations, making managing of sales easier. Plus it can help you analyze sales results.

QuickBooks Online by OneSaas Highlights:

• Create different customer groups and assign orders to those groups.
• Match QuickBook Online product items by name or SKU.
• Keep a track of payments that are made to you by Shopify.
• Can match tax codes between apps.

Our second entry into a short list of those that can both manage QuickBooks and Xero integration. What makes this app slightly different is that not only can it handle QuickBooks Online, but also QuickBooks Desktop. Therefore, it’s one of the most versatile Shopify accounting apps on offer.

Inside the app, which is used by more than 10,000 businesses, it can sync your orders within your schedule. It can summarize these by day, week or month. It can also update your inventory, so when a sale or return is made, you know exactly what you have left in stock. If there are missing products, which are sold on Shopify but not included within your QuickBooks, then the app will automatically create the product for you within QuickBooks. The app can also handle bundled items and returns.

This accounting app will also help keep Shopify related fees separate from other fees and keeps them as a bill transaction. This allows you to see how valuable Shopify services are for your business.

The app is fully compliant with sales tax, even if the business sells in multiple tax jurisdictions, making it the perfect app for those who sell across countries, or across states within the United States.

QuickBooks Online/Xero Sync Highlights:

• Works across three different accounting platforms, great for those who use QuickBooks Online, Desktop or Xero.
• Creates missing products when they’re not in your accounting system.
• Works across accounting jurisdictions.
• Syncs your inventory and financial data.

This app allows you to accurately analyze how profitable your store is quickly so you can make necessary adjustments to keep profits where you want them to be. With this app you can see prices for products, shipping and transactions, cost of ads and software subscriptions. You can see all these expenses on one easy dashboard enabling you to keep track of all your costs.

This app will help you save time without manually analyzing all your costs such as advertising, shipping and products and will have all this information for you. It integrates with a variety of advertising platforms such as Facebook, Google and Printful to name a few.

Accountify: Real Time Profit Highlights

• Manage advertising and subscription costs.
• Quickly analyze the profitability of your store.
• Itemize profits from individual orders.
• Manage expenditure on apps.

This accounting app is in German and will enable you to export accounting data at the end of the month which you can then send to your accountant. The data will include sales made, refunds, discounts and shipping. The data can be sent as either a CSV file or in DATEV format which is German standard for tax consultants.

You can have up to three shops on your account but will need to contact the developers if you are a B2B store or multichannel. This app is mostly ideal for Shopify stores selling to customers and generally suits merchants with over 100 orders per month.

Accountingexport Pro > DATEV Highlights

• Software in German only.
• Can export the data for your accountant to use.
• Includes sales, refunds, discounts etc.
• Support included such as onboarding sessions and email.

Unlike some of the other entries on this list, this doesn’t connect your store to QuickBooks or Xero, this one is for FreshBooks. FreshBooks is considered to be an easy-to-use accounting software system that anyone can use. And it has many of the same features that you would expect in an online accounting system.

This app will allow you to pull existing order history automatically into your FreshBooks account. The data can be synced several ways which include as one new client under your company name, into an existing client name within FreshBooks or as new client for each Shopify customer.

When an order is made, an invoice will be created within FreshBooks. The invoice will include all items sold and then will have the payment applied to the invoice. All information can be manually or automatically synced.

FreshBooks Highlights:

• Uses FreshBooks as the accounting software.
• Three options to create user data.
• Easy to use accounting software.
• Can be automatically synced.