Best Shopify Bookkeeping Apps

25 Best Bookkeeping Apps for Shopify in 2026

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...
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...
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 ...
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 ...
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...
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...
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 ...
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 ...
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...
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...
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...
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 ...
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...
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...
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...
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, ...
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...
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...
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...
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...
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...
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...
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...
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...
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...

Shopify Bookkeeping Apps

We know it is easy to choose the best solution between the Shopify Bookkeeping apps. With so many options to choose from, it's hard for entrepreneurs like you who are running an e-commerce business and trying to find the best Bookkeeping apps that will fit your needs and help you with your Shopify store.

The great news is that we have done all the research for you so that you don’t have. We have curated an epic list to save you time and headaches! We have listed all the best Shopify Bookkeeping apps. There are 25 Bookkeeping solutions for Shopify on the list at the moment and we will keep adding new ones as the market.

We also constantly update the data to help you with your choices!