If you’re still manually moving order details from your Shopify store to QuickBooks, you’re likely looking for a better ecommerce accounting sync solution.
The ideal integration can automate order syncing, refunds, fees, taxes, customers, and inventory, but the options vary greatly. Some are dedicated Shopify–QuickBooks apps, while others require you to develop and manage your own workflows. Compatibility also differs between QuickBooks Online and QuickBooks Desktop.
We look at the best Shopify integration software options for QuickBooks, focusing on features, pricing, setup, and which ecommerce businesses they serve best.
TL;DR: The Best Shopify-QuickBooks Integration Options
| Tool | Best For | Starting Price |
| MyWorks | Shopify merchants on QuickBooks Online or Desktop who want a dedicated, real-time sync | Free forever on QuickBooks Online (Launch, 20 orders per month); paid from $19 per month (Rise, billed annually) |
| Zapier | Merchants who want to build their own automations across other tools, not just QuickBooks | Free (100 tasks per month); paid from $19.99 per month |
| Skyvia | Merchants who need to sync other data sources alongside QuickBooks | Free (10k records per month); paid from $79 per month |
| QuickBooks Online Connector (by Intuit) | Small, Shopify Payments-only stores that want a free starting point | Free with a QuickBooks Online subscription |
| BOLD QuickBooks Sync PRO | Stores that want a dedicated Shopify-QuickBooks app as an alternative to MyWorks | From $19.99 per month |
1. MyWorks: Two-Way Sync For Shopify and QuickBooks
MyWorks is the fastest way to sync your Shopify store with QuickBooks. It’s managed in your store’s backend, so you don’t have to switch between platforms to access your e-commerce accounting information. It also supports quick automap by name or SKU (stock keeping unit).Â
MyWorks holds Built for Shopify status and recognition as an Intuit Platinum Partner, the top tier in Intuit’s App Partner Program. It also works with both QuickBooks Online and QuickBooks Desktop through a separate dedicated app for Desktop users.
If you’re selling in different currencies, that’s not a problem. With MyWorks, you can configure data in multiple currencies in your QuickBooks or Shopify account. It works with all Shopify payment gateways: Shopify Payments, PayPal, Stripe, and more, so you won’t miss a transaction.
MyWorks Top Features
- Backend integration: MyWorks is the most efficient e-commerce accounting integration software that lets you manage QuickBooks accounting from the backend of your Shopify store. That way, you don’t have to jump from one platform to another multiple times in a day.Â
- Ease of setup and use: you don’t need any complex technical knowledge to sync your QuickBooks and Shopify accounts with MyWorks. Once you’ve set it up, it keeps working automatically.
- Flexibility: MyWorks gives you complete control over how and when your order data syncs. You can set the order sync frequency depending on your e-commerce accounting needs.
You can also sync orders as estimates, receipts, or invoices. Or categorize order data based on pre-mapped categories, products, or variation levels.
- Two-way sync: Sync your product data both ways. Update inventory or pricing in QuickBooks, and it will automatically sync to Shopify.
MyWorks Pricing
QuickBooks Online:
- Free-forever Launch plan that syncs up to 20 orders per month.
- Paid plans (billed annually) start at $19/month with Rise for up to 100 orders.
- Grow at $39/month for up to 300 orders.
- Scale at $79/month for up to 1,000 orders.
- Soar at $99/month for unlimited orders.
QuickBooks Desktop:
- Rise $69 per month.
- Grow $89 per month.
- Scale $109 per month.
- Soar $139 per month.
- Prices listed are annual billing, and plans include a 14-day free trial.
Check out MyWorks full pricing breakdown to see what you get with each plan.
2. Zapier: No-code Shopify-QuickBooks Integration
Zapier lets you create custom integrations for Shopify and QuickBooks. For example, you can create a zap (automation) that adds a new customer in QuickBooks when a new customer orders via your Shopify store. It also has integration templates you can tweak to fit your needs (if you don’t want to set things up from scratch).
Building these integrations manually can be time-consuming, especially if you’re new to the tool and not tech-savvy. Also, the support team isn’t always available to answer questions, which can be a deal breaker for smaller e-commerce businesses looking for hands-on support.Â
Zapier Top Features
- Done-for-you templates: you don’t have to set up your Shopify-QuickBooks integration from scratch. Simply choose one of Zapier’s customizable integration templates and tweak it to fit your needs.Â
- Customization: you can build custom integrations for your Shopify and QuickBooks accounts if none of the templates match what you’re looking for.Â
- Scalability: Zapier adapts to your automation demands. You can add more Zaps as your store expands, avoiding a strict limit. However, increasing Zaps affects manageability; the more you use them, the more challenging it becomes to monitor the entire setup.
Zapier Pricing
- Zapier has a free plan with 100 tasks per month.
- Paid plans start with Professional at $19.99 per month, which adds multi-step Zaps, unlimited premium apps, and pricing that scales by task volume.
- Team plans start at $69 per month for shared workflows across a group.
- Enterprise pricing is available by quote.
3. Skyvia: Cloud-Based Integration for Shopify and QuickBooks
The Skyvia Shopify-QuickBooks integration automates data transfer between the two platforms. You can set up custom workflows in QuickBooks to create invoices for every new order in Shopify, update inventory levels in QuickBooks based on Shopify sales, and sync customer data. You can also apply filters, perform data calculations, or adjust data formats to meet the specific requirements of your Shopify and QuickBooks setup.
Skyvia is managed outside Shopify, so you’re maintaining three platforms instead of one. QuickBooks, Shopify, and the connector itself all require separate attention beyond your core ecommerce responsibilities. A native QuickBooks-Shopify integration like MyWorks, on the other hand, lives in your Shopify backend so you can manage both sales and accounting from one place.
Skyvia Top Features
- Integrations library: in addition to QuickBooks and Shopify, Skyvia supports CRM tools and e-commerce software such as WooCommerce. This provides multiple options for building custom accounting workflows for your e-commerce business.Â
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- Customizable data handling: it offers options to apply filters, perform calculations, or adjust data formats during the integration process to meet the unique requirements of your Shopify and QuickBooks setup.
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- Custom field mapping: Skyvia allows you to map fields from one platform to corresponding fields in another, ensuring that data is accurately transferred. For example, you can map customer names, email addresses, and order details from Shopify to the appropriate fields in QuickBooks.
Skyvia Pricing
- Skyvia’s free plan covers 10,000 records per month across up to 2 scheduled integrations.
- Paid plans start at $79 per month billed annually (or $99 month-to-month) for daily scheduling and 5 integrations, and scale up to $399 per month annually for per-minute scheduling and unlimited integrations.
- Skyvia also sells automation and backup as separate products from data integration, so check which one you actually need before you commit.
4. QuickBooks Online Connector (by Intuit): Free Sync for Shopify Payments Stores
This is Intuit’s own native app for connecting your Shopify store to QuickBooks Online. It syncs sales, payments, and fees, and maps categories automatically for your balance sheet and account statements. It’s free to install; you just need your own QuickBooks Online subscription, and it can automatically reconcile up to 12 months of activity.
It’s a narrower tool than the dedicated apps above, though. It’s built around Shopify Payments specifically, so other payment gateways may not be reliably captured, and it doesn’t import customer information the way a dedicated sync does.
QBO Connector by Intuit Top Features
- Sync historical data: automatically reconcile up to 12 months of Shopify activity in QuickBooks Online.
- Category mapping: sales, taxes, and fees are mapped to the right accounts automatically, cutting down on manual entry.
- Native Intuit support: built and supported directly by Intuit, with no separate connector fee.
QBO Connector by Intuit Pricing
Free to install with any QuickBooks Online subscription. There’s no separate connector fee.
5. BOLD QuickBooks Sync PRO: In-App Shopify-QuickBooks Integration
BOLD QuickBooks Sync PRO (formerly QuickBooks Sync by Bold) has been around for over a decade and has been tested by many merchants for their syncing needs.
It supports automated order imports and inventory management, among other features. It also provides 24/7 customer support and a knowledge base where you can find troubleshooting documents.
Bold QuickBooks sync PRO is a dedicated Shopify-QuickBooks option, priced per order instead of a flat rate. Reviews are mixed on reliability at scale, so it’s worth testing on the 14-day trial with your real order volume first.
BOLD QuickBooks Sync PRO Top Features
- Flexible order syncing: Sync product and inventory data from QuickBooks into Shopify directly. You can also import orders and refunds from Shopify into QuickBooks.Â
- Customer management: Import and manage customer data in QuickBooks.Â
- Export data on demand: Move your data to and from QuickBooks and Shopify whenever you want. You can also set up recurring data syncing.Â
BOLD QuickBooks Sync PRO Pricing
- Starter Plan: $19.99 per month and lets you sync up to 200 orders (then $0.15 per additional order, up to a $99.99 monthly cap).
- Growth Plan: $39.99 per month for up to 500 orders (then $0.10 per additional, same cap).
- Enterprise Plan: flat $59.99 per month for unlimited orders.
- All plans include a 14-day free trial.
What To Consider When Choosing a Shopify Integration For QuickBooks
The Shopify integration you choose depends on your specific business needs. On a high level, you should prioritize the following when evaluating the available options.
Syncing Accuracy
Make sure the integration accurately syncs data between Shopify and QuickBooks. This includes orders, inventory, customers, and financial data. Look for features like real-time syncing to minimize errors and discrepancies. Positive customer reviews are also a good sign that the integration is reliable and bug-free.
Support and Updates
Check if the provider offers helpful customer support if you need assistance. Also, see if they regularly update the integration to keep it working smoothly with Shopify and QuickBooks. This ensures you have someone to turn to if you encounter problems and that the integration stays reliable over time.
Pricing
Consider the pricing of the integration, including any additional costs for extra features or support. Choose an integration that fits within your budget and offers the features you need to grow your business.
Which QuickBooks Your Ecommerce Store Uses (QBO/QBD)
QuickBooks Online and QuickBooks Desktop are different products, and not every tool on this list supports all of them. If you’re on Desktop, confirm that upfront rather than assuming it’s covered.
Running B2B or wholesale too? This guide covers the general Shopify-QuickBooks sync. For tools built specifically for wholesale operations, see our best Shopify wholesale apps guide.
MyWorks: The Best Shopify Integration Software For QuickBooks
If you’re looking for Shopify integration software that offers full-on customization features while automating tedious accounting tasks, MyWorks is definitely one to try. What makes MyWorks stand out is its two-way sync, excellent customer support, and extensive e-commerce integration features.Â
Don’t just take our word for it. Here’s what one of our customers says about syncing Shopify and QuickBooks with MyWorks.Â
I’ve been so happy with MyWorks, and the amazing support has been just the icing on the cake. I’m so impressed with the attention to detail and how much control I have over what syncs with QuickBooks — like mapping my products and variations however I need to, syncing some orders to a single QuickBooks customer, and how the automatic sync just works so quickly (which is always important for inventory). I had some custom data that I needed to have shown in the QuickBooks Sales Receipt, and the custom field mappings were able to bring that over perfectly for me.
Book a free demo to see our Shopify and QuickBooks integration software in action.Â
Shopify Integration Software For QuickBooks FAQsÂ
Find answers to common questions about syncing QuickBooks and Shopify.Â
1. What is the Best Way to Integrate Shopify With QuickBooks?Â
MyWorks is the best Shopify-QuickBooks Integration software. The sync supports two-way data syncing in real time, flexible data mapping, as well as advanced settings to customize the sync to your business needs.
2. What is Integration Software?Â
Integration software is used to connect two or more separate software applications or systems so that they can share data and work together seamlessly. The data gets transferred between different applications, often in real-time, without the need for manual intervention. A good example is Shopify integration software for QuickBooks.
3. What is QuickBooks?Â
QuickBooks is a popular accounting software that helps businesses manage their finances. It is widely used for invoicing, expense tracking, payroll management, and tax filing.
4. What is Shopify?Â
Shopify is a popular e-commerce platform allowing businesses to create online stores and sell products or services. It provides a user-friendly interface for building and customizing an online store, managing inventory, processing payments, and tracking orders.
5. Why Do You Need to Sync Shopify and QuickBooks?
Syncing Shopify and QuickBooks lets you automate data transfer between both platforms. This saves time and reduces errors by streamlining your accounting processes and keeping inventory levels accurate. You can quickly and easily access important data like sales and expenses with real-time syncing.
