Seamless ERP Integration

ShipStation QuickBooks Integration

Connect ShipStation with your accounting and ecommerce systems to reduce manual work, eliminate errors, and keep your operations and financial data aligned.

Trusted by ERP administrators and retail operations teams globally.

ChatGPT Image Jun 24, 2026, 01_32_12 PM

ShipStation QuickBooks Integration Summary

Connect ShipStation with your ecommerce and accounting systems to automate order syncing, fulfillment updates, and financial workflows. Eliminate manual data entry while keeping orders, inventory, and accounting in sync.

What Data Does Connex Sync?

Explore how data flows between ShipStation and QuickBooks.

Data Type SYNC DIRECTION Frequency
Products ShipStation QuickBooks Real Time
Inventory ShipStation QuickBooks Real Time
Orders Two Way Sync Real Time
Customers ShipStation QuickBooks Real Time
Refunds ShipStation QuickBooks Scheduled
Fulfillment ShipStation QuickBooks Scheduled
Taxes ShipStation QuickBooks Scheduled

Built for Complex ShipStation Workflows

Everything you need to automate fulfillment, accounting, and ecommerce operations.

Sync Orders & Fulfillment

Automatically sync ShipStation orders, tracking numbers, fulfillment status, and shipping updates with your accounting system to eliminate manual data entry.

Built for Complex Workflows

Handle multi-channel orders, custom business rules, and advanced fulfillment processes that standard integrations can't support.

Accurate Accounting

Map transactions to your accounting structure, reduce reconciliation errors, and keep your ecommerce, fulfillment, and financial data perfectly aligned.

Testimonials

"Connex is handling our setup very well and support has been responsive. It was relatively straightforward to confirm (prior to purchase) how the systems architecture could work, and I've had very few surprises once I dove in to get it going.

Mark Carpenter
Founder
Gentent
12 (1)

"I love that Connex is flexible, customizable, and reliable. It just works, so I don’t ever have to think about syncing my inventory and sales orders from Shopify to QuickBooks. It seems like my accounting team has infinite options for tailoring the connector to our specific needs."

Kate Harvey
CoFounder
Bare Bones Broth
10 (2)

I did research after research. Once I came across ShipStation and found that Connex could connect all parts of my workflow, the puzzle finally came together. It’s a domino-effect. Once my job became easier, the pressure has been taken off other people as well. Connex just works and I don’t have to think about it. With Connex, the door opened up for the full ecommerce experience.

Mitch Hollander
Vice President
Bare Bones Broth
Mitch-Hollander

It is easy to map our order types. Connex is also user-friendly with the set-up, and support is always helpful. The Connex Team has also been great when needed.

Allie Wightman
COO
Fair Harbor
MicrosoftTeams-image (7)

Loaded Boards has been using Connex since 2015. It has greatly streamlined our processes and runs seamlessly.  We're big fans and recommend Connex highly to anyone using Quickbooks Enterprise and one or numerous channels.

Don Tashman
Founder and CEO
Loaded Boards
DonTashman

Really glad that we selected this app to sync Shopify with QuickBooks Online. Works seamlessly, and VERY helpful support staff. What I personally really appreciate is the level of customer service provided. They are easy to reach, and very patient with people like me who are new at needing to keep track of online sales.

Scott Mitchell
CEO
Simply Organic
13-1

Our main reason for using Connex was to save time from doing manual data entry. It worked really well for my client, Chinook Farms, so I recommended it to Bare Bones Broth. Once we had Connex running, operations at Bare Bones went much more smoothly. Connex takes only a few hours to set up and run. My favorite part is that it takes care of all the manual work and captures all the important details for accounting.

Emily Imbach
Founder
Embach Solutions
4 (3)

We are stoked on Connex and what it provides. It is mission-critical to have invoices and inventory integrated between Shopify and QuickBooks, and Connex gets it done! This was a solid upgrade from our previous Shopify to Quickbooks Desktop tool. Mostly because of the scheduler and ability to run the connection automatically. 

Troy Mothershead
Director of Planning and Business Development
True Ames Surf Fins
15-1

Your product allowing us to keep our Shopify store and QBO accounts, sales & inventory all properly synced continues to be a real help and appreciated value. As well, I would also like to say – as we are a small and not terribly tech-savvy team – your customer service and troubleshooting on the rare occasions we have needed it – has been exemplary.

James Satloff
CEO
Liberty Skis
15-1

We love Connex because it’s very hands-off. Matching deposits is a huge feature, and being able to do this properly is amazing! Financial visibility is incredibly important for us as a small business and being able to see this in real-time is a bonus. We plan on using Connex for years to come while we grow our business!

Jon Chastney
CEO and Co-Founder
First Scout.tv
8 (3)

When making business decisions, I had to keep in mind that my cost of goods sold (COGS) was different on different sales channels. Keeping the books up to date would have been impossible to do without Connex.

Petruziello
Seller on Amazon, Shopify, WooCommerce
Point One International
7 (1)

I depend on this software. I only have to keep my QB inventory up to date and it’s nice that my website will display accurate inventory. In the past, I have had to update both my QB and my Website. It would take hours a week. Connex saves time by automatically updating inventory and importing orders into QuickBooks.

Louisa Ngum
CEO
Honey Girl Hawaii
11 (2)

Before Connex, we had to manually enter all our orders from QuickBooks, which was very tedious and prone to human mistakes. We are extremely happy with Connex and we are in the process of finishing our online store, which we will be also using Connex to integrate. Connex streamlined our full operation & saved countless hours!

Jose Doimeadios
Director of Ecommerce
American Petroleum Services
9 (2)

Sync with Connex has been a huge time-saver for us. Having our financial automated is invaluable! What I like most about Connex is their Rules Engine and the flexibility they provide in running my business.

Dave Lavigna
Founder
The Sound Parcel
3 (6)

Overall, Connex has saved our company thousands of hours and we wouldn’t be able to survive without it! The software pays for itself since we were manually processing all our website and Amazon orders into Quickbooks. Now with it automated, we no longer have any accounting errors! I highly recommend this for anyone who does a large number of Amazon or Shopify orders! 100% worth every penny!

Conrad Martin
Director of Customer Service
Breeo
2 (4)

Thank you for your continued support of the CONNEX product. As our business has been growing, and transaction volume increasing, Connex has not given us one hiccup!Once again, thank you for the wonderful product and support!

Alex Esnaola
CFS, Products Inc.
CFS, Products Inc.
1 (6)

We had no way to communicate QuickBooks with ShipStation. Now Connex has bridged the gap between all of Soap and Paper Factory’s outsourced locations. Connex has totally changed our world. We are moving to Amazon, and because of Connex we can!

Shannon Burch
Co-founder
Soap & Paper Factory
14 (2)

Having one solution that connects with our BigCommerce platform and QuickBooks was great! We have a very strict inventory list and Connex was just the smoothest product out there that was functional and easy to use.

Hilary Famolare
CEO and Owner
Bordertown Farms
Hillary-1

Optimized for Your Operations

ShipStation orders automatically syncing to QuickBooks with customer, product, and order details.

Summary Sales Without Journal Entries

Automatically summarize shipped orders into QuickBooks while still relieving inventory and recording cost of goods sold. Avoid the limitations of journal entries and keep your financial reporting accurate.

Tracking numbers and fulfillment status syncing automatically between ShipStation and accounting software.

Accurate Shipping & Accounting

Sync shipped orders, tracking information, shipping charges, and fulfillment status with QuickBooks so your accounting reflects what was actually shipped.

Custom workflow rules for ShipStation orders, shipping methods, and accounting automation.

Inventory Relief & Cost of Goods Sold

Reduce inventory automatically as orders ship and ensure cost of goods sold is recorded correctly—without manual adjustments or spreadsheets.

Frequently Asked Questions

Can ShipStation sync with QuickBooks?
Yes. Connex automatically syncs ShipStation orders with QuickBooks, reducing manual data entry and keeping your accounting records accurate. You can also sync tracking numbers and fulfillment updates back to QuickBooks to maintain complete order visibility.
What data can Connex sync between ShipStation and QuickBooks?
Connex can sync customers, products, sales orders, invoices, payments, shipping details, tracking numbers, taxes, and fulfillment status. Flexible mapping options let you customize how data is posted in QuickBooks to match your accounting workflow.
Does Connex support complex ShipStation workflows?
Yes. Connex is built for businesses that have outgrown basic integrations. Whether you sell across multiple channels, use custom fulfillment processes, or require advanced accounting rules, Connex can automate workflows that standard connectors often cannot handle.
How long does it take to set up the ShipStation and QuickBooks integration?
Most customers can get started quickly with the help of our onboarding team. Connex specialists guide you through setup, configure your workflow, and ensure your ShipStation and QuickBooks integration is working correctly before you go live.

Ready to Automate ShipStation and QuickBooks?

See how Connex can eliminate manual data entry, simplify fulfillment, and keep your accounting accurate with a workflow built for your business.