Best Shopify Quickbooks Integration Roundup

in QuickBooks Integration · 7 min read

Laptop showing accounting dashboard on desk

Compare top Shopify apps that sync Shopify with QuickBooks and QuickBooks Desktop. Ratings, pricing, screenshots, and quick verdicts for merchants

This roundup compares leading Shopify apps that integrate Shopify with QuickBooks Online and QuickBooks Desktop. It highlights pricing, ratings, screenshots, and which merchants each app suits best.

Use this to pick an integration if you want automated sales, fees, payouts, and inventory sync between Shopify and QuickBooks systems.

RankAppBest ForRatingReviewsPricingNotable
1!App Icon Xero & QuickBooks Smart SyncAutomating invoice and payout adjustments⭐⭐⭐⭐⭐64$9/moAuto creates invoices and adjustments for payouts, orders, customers and fees
2!App Icon QuickBooks Online GlobalMerchants selling outside the US and multi-store setups⭐⭐⭐⭐⭐2773$30/moDesigned for international storefronts and multiple Shopify stores
3!App Icon QuickBooks Sync by MyWorksDeep, trusted QuickBooks sync for e-commerce⭐⭐⭐⭐⭐31$24/moTop-rated sync trusted by e-commerce business owners
4!App Icon QuickBooks OnlineBasic sync of products, orders and payouts to QBO61Free to installSyncs sales, fees and inventory into QuickBooks Online
5!App Icon A2X Sync for QuickBooks & XeroAccurate accounting for merchants and bookkeepers⭐⭐⭐⭐⭐313$29/moTrusted by accountants and bookkeepers for accuracy
6!App Icon eBay Integration - DPLSellers syncing marketplaces with Shopify⭐⭐⭐⭐⭐643$19.99/moMarketplace sync that supports products, inventory, and orders
7!App Icon Etsy Integration - DPLEtsy sellers who also use Shopify⭐⭐⭐⭐⭐618$19.99/moSyncs product, order, and inventory between Shopify and Etsy
8!App Icon 4PsiteLink (4P)Centralized order management across marketplaces⭐⭐⭐⭐⭐2Centralizes Shopify and 40+ marketplaces into an OMS
9!App Icon Etsy Integration - CedCommerceEtsy marketplace automation at scale⭐⭐⭐⭐⭐1141$9/moAutomates inventory, listings and sync with Etsy
10!App Icon DPL Square IntegrationRetail stores using Square and Shopify⭐⭐⭐⭐⭐138$39.99/moTwo-way inventory sync between Square and Shopify
11!App Icon Webgility x QuickBooks DesktopQuickBooks Desktop users needing reliable sync⭐⭐⭐⭐⭐397$139/moConnects Shopify to QuickBooks Desktop for orders, expenses and payouts

1) Xero & Quickbooks Smart Sync

!Xero & QuickBooks Smart Sync Icon

Goodbye manual adjustments: Reconciley automatically creates invoices and adjustments for payouts, orders, customers and all fees with Xero & Quickbooks (QBO).

Rating: ⭐⭐⭐⭐⭐ (4.7/5)

Reviews: 64

Pricing: $9/mo | $9 | $90

Best for: Merchants who need automated invoice and payout adjustments to match Shopify payouts to QuickBooks.

Short verdict: Strong automation for reconciling payouts and fees into QuickBooks and Xero, ideal if you want fewer manual journal entries.

2) Quickbooks Online Global

!QuickBooks Online Global Icon

Easily manage the connection between Shopify and QuickBooks Online. For merchants that sell outside of US, connect all of your Shopify storefronts …

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 2773

Pricing: $30/mo | $55/mo | $30 | $55

Best for: Multi-store and international merchants who need a robust connection to QuickBooks Online across regions.

Short verdict: High-volume, well-reviewed option for global sellers needing consistent QBO sync across storefronts.

3) Quickbooks Sync by Myworks

!QuickBooks Sync by MyWorks Icon

Forget manual bookkeeping and save 100s of hours with MyWorks. The top-rated QuickBooks Sync, trusted and loved by thousands of e-commerce business owners.

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 31

Pricing: $24/mo | $24 | $228 | $49/mo

Best for: Merchants who want a feature-rich, trusted sync built specifically for e-commerce flows.

Short verdict: Reliable and tailored for merchants who need a comprehensive QuickBooks sync that reduces manual bookkeeping.

4) Quickbooks Online

!QuickBooks Online Icon

Sync products, orders and payouts into QuickBooks Online to record sales, fees and update inventory.

Rating:

Reviews: 61

Pricing: Free to install

Best for: Merchants who want a simple, no-cost way to get basic sales and payout data into QuickBooks Online.

Short verdict: Basic official QuickBooks Online connector for straightforward syncing. Good starting point for simple stores.

5) A2X Sync for Quickbooks & Xero

!A2X Sync for QuickBooks & Xero Icon

Join the thousands of merchants, accountants, and bookkeepers that trust A2X to accurately automate their Shopify accounting in QuickBooks Online or Xero.

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 313

Pricing: $29/mo | $45/mo | $29

Best for: Merchants and accountants focused on accuracy of revenue recognition and fee allocation in QuickBooks or Xero.

Short verdict: Accurate, accountant-friendly solution for mapping Shopify payouts and marketplace fees into accounting platforms.

6) Ebay Integration - DPL

!eBay Integration - DPL Icon

Shopify eBay Integration app. Sync Products, Inventory, and Orders between the Shopify and eBay stores in real-time.

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 643

Pricing: $19.99/mo | $29.99/mo | $19.99 | $29.99/mo

Best for: Sellers running both Shopify and eBay channels who want real-time inventory and order sync.

Short verdict: Strong marketplace sync that helps ensure accounting data is consistent across channels before posting to QuickBooks.

7) Etsy Integration - DPL

!Etsy Integration - DPL Icon

Shopify Etsy Integration app - Best way to sync your online Shopify store with Etsy Store.

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 618

Pricing: $19.99/mo | $28.99/mo | $19.99

Best for: Etsy sellers using Shopify as their central storefront who need synchronized listings and inventory.

Short verdict: Practical tool for Etsy-Plus-Shopify sellers; keeps listings and stock aligned for cleaner accounting.

!4PsiteLink (4P) Icon

4Psite centralizes your Shopify stores, as well as over 40 marketplaces, into a fully integrated order management system. Streamline your processes…

Rating: ⭐⭐⭐⭐⭐ (5/5)

Reviews: 2

Pricing:

Best for: Businesses that need a centralized order management system across many marketplaces and Shopify stores.

Short verdict: Useful OMS for complex multi-marketplace merchants who then push consolidated transactions into QuickBooks.

9) Etsy Integration - Cedcommerce

!Etsy Integration - CedCommerce Icon

Seamlessly integrate your Shopify store with Etsy. Automate inventory management, sync listings and boost sales with the Etsy Marketplace Integration app.

Rating: ⭐⭐⭐⭐⭐ (4.8/5)

Reviews: 1141

Pricing: $9/mo | $29/mo | $9

Best for: Merchants who need affordable Etsy syncing with Shopify and basic automation for listings and inventory.

Short verdict: Cost-effective Etsy connector for shops that need reliable marketplace-to-Shopify sync before accounting.

10) DPL Square Integration

!DPL Square Integration Icon

DPL - Square Integration & Sync allows you to seamlessly integrate Square and Store for smooth product import, export, and both-way inventory sync.

Rating: ⭐⭐⭐⭐⭐ (4.8/5)

Reviews: 138

Pricing: $39.99/mo | $59.99/mo | $39.99

Best for: Brick-and-mortar retailers who use Square for POS and Shopify for online sales and need consolidated accounting.

Short verdict: Good option for retailers whose QuickBooks records need consistent Square and Shopify transaction data.

11) Webgility X Quickbooks Desktop

!Webgility x QuickBooks Desktop Icon

Webgility connects Shopify to QuickBooks Desktop, so orders, expenses, payouts and inventory are accurate without any manual work.

Rating: ⭐⭐⭐⭐⭐ (4.9/5)

Reviews: 397

Pricing: $139/mo | $249/mo | $139

Best for: Merchants still on QuickBooks Desktop who need a robust connector that handles orders, payouts, fees and inventory.

Short verdict: Leading choice for QuickBooks Desktop users wanting automated, reliable syncing to reduce manual reconciliation.

How to Choose

  • Accounting target: Choose QuickBooks Online connectors for cloud accounting, or Webgility for QuickBooks Desktop.
  • Volume and complexity: For high-volume stores and multi-store setups, prefer QuickBooks Online Global or MyWorks.
  • Fee and payout handling: Pick apps that explicitly reconcile payouts and fees (Xero & QuickBooks Smart Sync, A2X).
  • Budget and trial: Start with free or lower-cost connectors to validate mapping before committing to expensive plans.
  • Marketplace sync: If you sell on eBay or Etsy, use a marketplace connector that syncs inventory to prevent double-counting.

Common Mistakes

  • Assuming all apps map fees and payouts the same way. Confirm how marketplace fees and refunds are recorded.
  • Skipping a test sync. Always run a parallel test period to validate accounts, tax codes and product mappings.
  • Ignoring multi-currency effects. International sales need currency handling in both Shopify and QuickBooks.
  • Relying on defaults. You will usually need to configure product, tax and payment account mappings.

FAQ

Do These Apps Support Quickbooks Online and Quickbooks Desktop?

Some apps focus on QuickBooks Online (QuickBooks Online Global, A2X, MyWorks) while others support QuickBooks Desktop (Webgility). Check each app page to confirm the specific QuickBooks edition supported.

How Do Apps Handle Shopify Payouts and Marketplace Fees?

Apps differ: some create consolidated payout invoices and adjustments (Xero & QuickBooks Smart Sync, A2X) while others post orders and fees separately. Verify the app maps fees and payouts in a way that matches your bookkeeper requirements.

Will Inventory Sync Affect My Quickbooks Stock Levels?

Yes. Most connectors update inventory in QuickBooks based on Shopify orders. Ensure SKU matching is accurate and run a full inventory reconciliation after initial setup.

Can I Use These Apps with Multiple Shopify Stores?

Yes. Apps like QuickBooks Online Global and 4PsiteLink are designed to aggregate multiple storefronts. Confirm pricing and configuration limits for multi-store use.

Sources & Citations

  • Xero & QuickBooks Smart Sync
  • QuickBooks Online Global
  • QuickBooks Sync by MyWorks
  • QuickBooks Online
  • A2X Sync for QuickBooks & Xero
  • eBay Integration - DPL
  • Etsy Integration - DPL
  • 4PsiteLink (4P)
  • Etsy Integration - CedCommerce
  • DPL Square Integration
  • Webgility x QuickBooks Desktop

Further Reading

Sources & Citations

Tags: quickbooks shopify accounting integrations
Jamie

About the author

Jamie — Founder, Profit Calc (website)

Jamie helps Shopify merchants build profitable stores through data-driven strategies and proven tools for tracking revenue, costs, and margins.

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