Best Shopify Bookkeeping Apps

25 Best Bookkeeping Apps for Shopify in 2026

McLedger

Complete accounting, bookkeeping, and VAT services for UAE entrepreneursWho is MCLedger? McLedger provides bookkeeping services for small businesses and startups in the UAE, and ...
GoBD‑Export

The GoBD-Export app helps you to export your store data, such as orders, products, users and more, for example if requested by the tax authorities. The data is compiled according ...
Accounting sync

Automated Bookkeeping and Reconciliation for Shopify, Trusted by Accountants Designed specifically for Shopify, our integration is designed to save you hours a day from having to ...
Ecominate

The missing piece to complete your e-commerce accounting stack Ecominate offers a powerful suite of analytics, inventory management, and accounting tools to streamline your e-comm...
Bench Accounting

With Bench, we do your bookkeeping for you—so you don’t have to. Unlike DIY software, there’s zero learning curve with Bench. Instead, you’re paired with a dedicated expert who kn...
QuickBooks Enterprise Sync

Webgility's Modern Commerce Workspace is designed to work with QuickBooks Pro/Premier/Enterprise and brings together all your commerce apps, like Shopify, Amazon, WooCommerce, Ets...
Finaloop

Shopify merchants enjoy 30 days of FREE services with Finaloop.Why Finaloop? Finaloop's dedicated accounting experts will get your books and taxes right for a fraction of the cost...
Accountingexport Pro > DATEV

Notice: Software available in German only! The Shopify data export for your accountant. Our software allows you to quickly export all accounting data at months end. It includes Sa...
Fortnox

Do your Fortnox bookkeeping effortlessly This connector app is a user friendly app for a very basic sync from your Shopify store to your Sweden based Fortnox billing and accountin...
E‑conomic link by CarryTheOne

Multiple Stores? No problem. You can connect multiple Shopify stores to a single E-conomic account*. Connect Shopify and E-conomic with CarryTheOne Link your Shopify store(s) with...
QuickBooks Online + Commerce

Manage everything from orders and inventory to bookkeeping with QuickBooks Commerce. Bundled with QuickBooks Online for more organized accounting, Commerce syncs with Shopify so y...
Quote Machine

About Quote Machine Are you selling high value products? Expensive traffic enters your site but leaves without buying? You’ve spent lots of time and effort to optimize the shopp...
KashFlow Integration by CTO

Multiple Stores? No problem. You can connect multiple Shopify stores to a single KashFlow account*. Connect Shopify and KashFlow with CarryTheOne Link your Shopify store(s) with K...
Niblin

Automate your accounting We have created Niblin to help you automate your accounting and bookkeeping. We create a bridge between your store in shopify and your account on xero or ...
FreshBooks Link by CarryTheOne

Multiple Stores? No problem. You can connect multiple Shopify stores to a single FreshBooks account*. Connect Shopify and FreshBooks with CarryTheOne As your business takes off, y...
PayTraQer

PayTraQer automates your bookkeeping with a simple interface, intuitive workflow and improved accuracy. With PayTraQer, you will always get perfectly balanced books, updated inven...
Streamlined

Streamlined – The best B2B invoicing solution for Shopify Streamlined was built to help fast-growing brands automate b2b invoicing, making it blazing fast and easy to manage. With...
Quaderno ‑ Taxes Automation

You didn’t start your business to be an accountant. To learn about the tax laws in various countries, to piece together the right invoices, to keep organized records for years and...
Bookkeep: Quickbooks/Xero Sync

Summarize Orders Into One Post, Sync to QuickBooks or Xero & Reconcile Payouts to Your Bank Feed—Automatically! You set up your account and chart of accounts once. We post a s...
QuickBooks Online Global

Save time and stay ahead of your bookkeeping when you integrate Shopify with QuickBooks Online International-only. Easily manage the connection between Shopify and QuickBooks Onli...
Xero or QuickBooks Sync

Finally, Shopify bookkeeping that’s accurate and automatic. Trusted by thousands of e-commerce sellers and leading accountants to ensure their bookkeeping is accurate, efficient, ...
BexioSync by BedayaConnect

Keep Shopify synchronized with bexio! bexioSync enables you to synchronize your Shopify customers, products, and orders with bexio. bexioSync removes the need for hours of manual ...
Email Invoice by Latori

This Ap will be switched off in March 2020.Monthly fees Our Basic Plan includes 30 days trial! Free: 50 emails (limited) - free Free Plus: 50 emails (free monthly fee + $0.07 for...
QuickBooks Online Sync

Webgility's Modern Commerce Workspace is designed to work with QuickBooks and brings together all your commerce apps, like Shopify, Amazon, WooCommerce, eBay, Etsy, and more. With...
IEX integration for Dinero

Connect Shopify and Dinero IEX connects Shopify and Dinero, sending orders, products (optional) and customers automatically from Shopify to your Dinero accounting system. That mea...

Shopify Bookkeeping Apps

With an ever-growing selection of Shopify Bookkeeping apps to choose from, finding the best Bookkeeping solution for your Shopify store can seem daunting. But have no fear - we've done all the hard work already!

We've curated a comprehensive list comprising 25 top Shopify Bookkeeping apps that offer impeccable integration with Shopify. Plus, our data is kept constantly up-to-date so you always get accurate information when it comes time to make those decisions about which app will suit your needs best and help take your e-commerce business even further.

p>Plus, you can trust us because we regularly update this data, so your decisions are based on up-to-date information. We strongly recommend reading the reviews while choosing the suitable Bookkeeping app for your Shopify store.