Best Free QuickBooks Connectors for Ecommerce

You chose a free QuickBooks connector to save money, but it's actually costing you thousands in hidden ways. Hours spent manually reconciling payments, inaccurate profit margins because fees aren't tracked, lost sales from inventory errors, and accountant bills that keep climbing because your books are a mess.

‘Free’ might sound appealing at first, but as your business grows or even as you prepare to scale, those free tools quickly show their limits. You’ll face restricted functionality, slow or unreliable syncing, one-platform compatibility, and little to no support when issues arise.

Finding a free yet reliable QuickBooks connector isn’t easy. This guide simplifies your search, explaining what each connector offers, when it makes sense to use one, and which use cases they’re best suited for.

By the end, you’ll know exactly when free tools fall short, and why smart sellers upgrade to Webgility to cut hidden costs and focus on growth.

Free QuickBooks connector line-up: Side-by-side review

Here’s a clear look at the free connector choices from major players. Let’s dive’deep into how they compare, and when they’ll start holding you back:

1. Shopify Connector by Intuit

Shopify Connector is a free tool that automates syncing of orders, products and inventory between your QuickBooks Online account and your Shopify store. It reduces manual bookkeeping and ensures accounting data stays current.

What it provides (Pros):

This connector covers the essential bases that most Shopify sellers need:

• Orders & refunds: each sale from Shopify flows into QuickBooks Online (QBO) with line-items
• Products & inventory: Updates to Shopify products feed into QBO; stock levels from Shopify reflected
• Customer information: Shopify contact details sync, enabling marketing or service tracking
• Taxes & shipping: Sales tax and shipping charge data captured for bookkeeping

For a brand-new Shopify store processing maybe 10-20 orders per month, this connector does exactly what it says on the tin. It's reliable, it's free, and it gets your basic data into QuickBooks without you lifting a finger.

The "Catch" (Cons):

• Limited customization of how data flows (for example- summarization choices are more basic)
• Every order is synced individually by default. This may flood your QBO with many line items and complicate reconciliation
• Support options are limited. Mostly email and community rather than white-glove

Bonus Read: Shopify Accounting: Best Practices That Simplify the Process

2. BigCommerce Connector by Intuit (aka "BFS")

The BigCommerce Connector by Intuit is a free integration that automatically syncs orders, products, customers, taxes, shipping, and discounts from BigCommerce to QuickBooks Online. It helps eliminate manual data entry and bookkeeping errors, with configurable workflows for mapping SKUs and accounts. Data typically syncs within about four hours, keeping your sales and accounting fully aligned.

What it provides (Pros):

The BigCommerce connector covers the essential automation needs that most BigCommerce merchants require:

• Automatically synchronises orders, products, customers, taxes, shipping, and discounts from BigCommerce to QuickBooks Online
• Setup is relatively quick and straightforward, with guided steps to connect BigCommerce to QuickBooks Online
• You can map how BigCommerce orders appear in QuickBooks (as invoices or sales receipts), and set default income/expense accounts and item/discount settings for better bookkeeping alignment

For a BigCommerce store just getting started, this connector provides basic automation.

The "Catch" (Cons):

• No built-in reporting or analytics
• Doesn’t sync COGS values automatically for new inventory items
• Can cause data mismatches or duplicates if item mappings and SKUs aren’t configured carefully

3. Myworks Sync Connector for WooCommerce

Myworks Sync Connector integrates WooCommerce with QuickBooks Online for syncing orders, customers, products, and payments between these two platforms. As a business grows and needs more features (e.g., higher order volume, faster sync times, advanced customization), you can easily upgrade to a paid plan.

What it provides (Pros):

MyWorks actually impresses with what they include:

• Product and inventory sync to keep systems aligned
• Global sales tax and multi-currency support
• Syncs transaction fees (e.g., Stripe, PayPal) as expenses for accurate net revenue

The "Catch" (Cons):

• The free plan caps at 20 orders per month
• Sync frequency is slower (usually hourly)
• Designed for micro or test stores, you’ll need to upgrade fast

4. Webgility QuickBooks Connector

Webgility QuickBooks Connector is a native Shopify application that directly integrates QuickBooks with Shopify to simplify and automate accounting for ecommerce businesses.
The tool enables faster, error-free syncing of sales, refunds, and payouts, eliminating manual data entry and the need for accounting expertise.

Key features:

1. Automation and syncing

• Transactional accounting: Posts Sales Receipts, Refund Receipts, and Expenses automatically
• Nightly sync: Automated nightly updates for continuous accuracy
• Historical sync: 3 months free, extendable up to 1 year for paid users
• Automated sales tax handling: Maps Shopify tax data to QuickBooks and leverages QuickBooks Automated Sales Tax

2. Data consistency & management

Ensures accurate and synchronized data between Shopify and QuickBooks.

Product catalog management:

• Automatically matches products via SKU or product name
• Allows auto-creation of unmatched products
• Filter by matched/unmatched status for visibility

Customer settings

• Option 1: Create & match individual customers for detailed reporting
• Option 2: Post all orders to a single default customer (for example- online sales), ideal for high-volume, one-time purchases

3. Deep customization controls

Users can tailor how transactions are posted:

• Set sync start dates and transaction numbering preferences
• Map Shopify payment gateways to QuickBooks clearing accounts
• Configure expense and payout fees to QuickBooks expense accounts
• Define whether items are inventory, non-inventory, or service types
• Enable or disable automation as needed

4. Dashboard & analytics

The dashboard offers a real-time financial overview:

• Sales This Month, Orders, and Pending Syncs metrics
• Sync Performance: 95%+ automated sync success rate
• Track cumulative synced orders, refunds, fees, and deposits for accountability and health monitoring

What it provides (Pros):

• Seamlessly syncs Shopify transactions (sales, refunds, fees, deposits) into QuickBooks Online
• Automates bank reconciliation, ensuring Shopify Payments and bank deposits match perfectly
• Provides real-time visibility into financials directly from Shopify
• Scales easily as sales volume grows, supporting evolving needs from 30 to 1,000+ monthly orders
  Offers email and live chat support

The "Catch" (Cons):

• Self-onboarding can be overwhelming for new sellers

Pricing

The pricing model is volume-based and flexible, making it suitable for businesses at every stage:

When to consider Webgility QuickBooks Connector-

• When your Shopify order volume passes 100 orders per month

A Quick Note: Choosing this tool streamlines data management by reducing reconciliation time, improving visibility, and keeping your records clean even as volumes grow. And if the free plan feels limiting, you can easily upgrade to a paid pay-as-you-go plan for advanced features.

• When you spend more than a few minutes reconciling payouts or bank deposits
• When you want automated nightly syncing and accurate mapping of Shopify taxes, fees, and refunds
• When you prefer all financial data to be visible from within Shopify, without manual review

Bonus read: Top 6 WooCommerce Accounting Software Compared for 2025

Free QuickBooks Connectors compared: Which one suits your ecommerce store? 

Before you plug in a free connector and hope for the best, here’s how the major players differ so you know what you’re really signing up for:

A few success stories to have a look at!

1. Skinny Mixes (Shopify + QuickBooks)

High-volume DTC brand, primarily on Shopify, manual bookkeeping was weighing them down. According to Webgility’s case study, after implementing their automation solution the brand:

• Boosted order volume by 75% year-over-year
• Added over $3 million in incremental annual revenue via expanded online growth
• Freed their team from manual data-entry, enabling them to focus on product innovation and customer experience

2. JVR Industries (WooCommerce + eBay + QuickBooks)

A vacuum-packaging specialist with multi-channel ambitions, JVR Industries were hindered by slow order handling and fragmented inventory/accounting workflows. After switching to Webgility:

• Order processing time dropped from 10 minutes per order to just 2 minutes
• Inventory and sales tax inconsistencies were eliminated via real-time integration of WooCommerce, eBay and QuickBooks
• Staff were freed to focus on innovation and growth instead of data entry

3. The Nappy Shoppe (Zen Cart + Amazon + Etsy + Brick-&-Mortar + QuickBooks)

A multi-channel baby-accessories retailer that was eight months behind on entering invoices, with full-time staff dedicated to manual entry. With Webgility:

• Saved approximately 52 hours per week in labour by automating orders, shipping workflows, and bookkeeping
• Shipping/fulfilment labour dropped by ~88%, enabling one-day shipping even during peak events
• Achieved up-to-date financials with far less friction (“We are now up-to-date with our finances and have stayed that way)

When to move beyond free connectors

Free tools are a great starting point, but you'll know it's time to upgrade when these pain points emerge:

• Your "Free" tool costs you time: You spend more time manually fixing sync errors, de-cluttering QuickBooks, or forcing manual syncs than you would have spent on a paid tool
• Your volume increases: You either hit a hard volume cap (like Myworks) or your QuickBooks file becomes so slow and bloated (like with the Shopify connector) that it's unusable
• Your accountant is unhappy: A clean set of books is vital for tax time. If your accountant can't make sense of your file, their billable hours will far exceed the cost of an automation tool
• You add a second sales channel: The moment you decide to sell on Amazon, eBay, or Etsy in addition to your website, free tools become a liability
• You can't trust your numbers: If you don't have clear visibility into your profitability, fees, and inventory, you can't make smart decisions to grow your business

What Webgility does differently:

With Webgility, you get the flexibility to post transactions individually or as summarized entries (daily, weekly, or monthly), keeping your books cleaner, more accurate, and fully reconciled from the start.

Webgility supports unlimited orders, real-time sync, and integrates WooCommerce with Amazon, eBay, and other channels, offering a unified, accurate accounting workflow.

This is when automation and detailed financial visibility become an investment, not an expense. The Webgility QuickBooks connector is the logical next step for sellers who have outgrown free tools and are serious about scaling their business.

Time to level up: Start automating with Webgility!

Choosing the right QuickBooks connector isn't about finding the cheapest option, it's about finding the right fit for your business stage. Free connectors like Shopify's native integration, BigCommerce BFS, and MyWorks serve a genuine purpose for new sellers processing limited orders on a single platform. They get your basic data into QuickBooks without upfront investment.

But here's what this guide reveals: the moment you exceed 100 orders monthly, add a second sales channel, or need clean books for tax season, free tools become expensive liabilities.

This is where Webgility helps by eliminating these growing pains with unlimited orders, 70+ platform integrations, intelligent order summarization, and real-time inventory sync, all backed by actual human support. Your QuickBooks file stays clean, reconciliation takes minutes instead of hours, and you get accurate profit visibility across every channel.

Ready to see the difference? Try Webgility free for 15 days and experience what true ecommerce accounting automation should feel like. 

Frequently asked questions (FAQs)

Do Shopify and QuickBooks integrate?

Yes, when Shopify is integrated with QuickBooks, it automatically syncs all your Shopify sales to QuickBooks Online. With one click, your complete order data, including line items, taxes, and payments, is seamlessly exported to QuickBooks for effortless, up-to-date bookkeeping.

Are free QuickBooks connectors worth using?

Yes, if you’re just starting out. They help small sellers sync basic sales data. But once order volume or channels grow, they create duplicate records and messy books, making a paid automation tool like Webgility a smarter investment.

How often do free connectors sync data?

Shopify and BigCommerce connectors sync hourly. However, some tools sync data nightly and limit historical data to seven days.