Yes, Shopify integrates with QuickBooks Online through SyncTools. The integration syncs Shopify orders, refunds, fees, taxes, COGS, and payout settlements into QuickBooks as clean journal entries or individual transactions. Categorize by country, product category, or sales channel. Setup takes under 15 minutes.
Trusted by Accounting and Finance Teams.
How the Shopify × QuickBooks Online Integration Works
SyncTools connects your Shopify store to QuickBooks Online using secure OAuth authentication — no passwords stored, no manual CSV exports. Once connected, Shopify transactions post to QuickBooks within minutes of occurring.
What syncs: Sales orders, refunds, payment gateway fees (Shopify Payments, Stripe, PayPal), Shopify platform fees, shipping charges, sales tax by jurisdiction, cost of goods sold (COGS), and payout settlements. Each item maps to the correct QuickBooks account in your chart of accounts — no guesswork, no manual journal entries after the fact.
Sync modes: Choose summarized sync — which consolidates daily Shopify activity into clean QuickBooks journal entries — or individual transaction sync that mirrors every order, payment, and refund one-to-one in QuickBooks. Summarized sync is ideal for high-volume stores; individual sync gives your accountant the granular detail they need for month-end close.
Unique categorization: SyncTools automatically categorizes income and expenses by country and state, product category, or Shopify sales channel (Online Store, POS, Facebook, YouTube). This gives you the most detailed P&L breakdown available in QuickBooks — far beyond what basic integrations offer.
Who uses it: Shopify merchants processing 200–5,000+ orders per month who need clean QuickBooks records. E-commerce accountants managing multiple Shopify clients from one dashboard. Growing DTC brands that need true profitability data with accurate COGS. Multi-channel sellers tracking revenue by source inside QuickBooks.
Pricing: SyncTools starts free — up to 200 orders per month, no credit card required. Paid plans start at $19/month (Lite), scaling to Standard ($59/month, 2,000 orders) and Plus ($89/month, 5,000 orders). All plans include the complete Shopify QuickBooks integration.
Two Ways to Sync Shopify with QuickBooks That Fits Your Business
Choose the sync method that works best for your workflow
Summarised Sync to QuickBooks Journal Entries
Consolidate sales, refunds, taxes, balances, and COGS into clean journal entries instead of cluttering QuickBooks with thousands of individual transactions.
Individual Transaction Sync to QuickBooks
Sync every Shopify order, payment, product, customer, refund, fee, and COGS individually into QuickBooks Online with perfect one-to-one accuracy.
Shopify accounting, stress free!
Comprehensive dashboard with real-time insights into your entire e-commerce operation
Auto-Categorize by Country and State
SyncTools automatically categorizes income and expenses by country and state, giving you highly accurate, detailed financial reports in QuickBooks Online.
- Simplify multi-region and multi-state accounting
- Gain deeper insights into profits and taxes by location
- Save hours on manual categorization and reporting
Know Which Products Drive Revenue
Organize income and expenses by product category to understand which items drive your revenue and keep your books structured in QuickBooks.
- Understand your top performing categories
- Organize books by product type, category, tags, or collections
- Easily create custom categories to suit your needs
Track Revenue by Sales Channel
Track income and expenses by Shopify sales channels and see a clear breakdown of where your revenue is coming from, all in one place.
- See performance across POS, Online Store, Meta, YouTube and more
- Accurately track sales, fees, and refunds per channel
- Get channel-level visibility inside QuickBooks
Effortless Reconciliation, Maximum Accuracy
SyncTools automatically matches Shopify payout deposits with your bank statements, eliminating manual work and reconciliation errors.
- 100% accurate matching of payouts and deposits
- Save hours on manual reconciliation
- Ensure error-free, clean financial records
Know Your True Profit
SyncTools consolidates sales, refunds, shipping costs, and inventory valuations to give you a clear picture of your true net profit with accurate COGS data.
- Sync all revenue and expense details seamlessly
- Track inventory value for accurate calculations
- Calculate true net profits with precise COGS data
Set up in just 3 easy steps
Get started in minutes with our simple setup process
Connect Your Accounts
Link your Shopify store and QuickBooks account with secure OAuth authentication in under 2 minutes.
Configure Settings
Choose your sync preferences, mapping rules, and automation settings with our guided setup wizard.
Start Syncing
Activate the integration and watch your data sync automatically in real-time. That's it!
How SyncTools elevates Shopify Commerce?
Powerful automation features designed for modern e-commerce businesses
Smart Reconciliation
AI-powered matching automatically reconciles transactions, saving hours of manual work every week.
Multi-Store Support
Connect multiple Shopify stores to a single QuickBooks account with separate tracking for each location.
Advanced Reports
Generate comprehensive financial reports with real-time insights into sales, expenses, and profitability.
Bank-Level Security
SOC 2 Type II certified with 256-bit encryption ensuring your financial data stays protected.
Manage your bookkeeping effortlessly
Choose the plan that fits your business needs
Compare Plans and Features
See which plan includes the features you need
SyncTools vs A2X vs Synder for Shopify QuickBooks
How the leading Shopify QuickBooks Online integration tools compare
| Feature | SyncTools | A2X | Synder |
|---|---|---|---|
| Starting price | Free (200 orders/mo) | $19/month | $19/month |
| Accuracy | AI-matched journal entries | Rule-based mapping | Transaction-level sync |
| Setup time | Under 15 minutes | 30–60 minutes | 30–45 minutes |
| Categorize by country/state | Yes — all paid plans | No | No |
| Categorize by sales channel | Yes — all paid plans | No | No |
| COGS tracking | Daily + monthly (paid plans) | Paid plans only | Partial |
| Support | Phone + Zoom + Email | Email only | Email + Chat |
Trusted by Teams Worldwide
Thousands of accounting firms and finance teams rely on SyncTools to streamline reconciliation and save hours every month.
Customers who are Trusting Us
Haider Ali
Business Owner
"Excellent app. Very easy to work with. Very knowledgeable, understanding, and open to any requests."
Tom Brookes
Finance Director
"Best in class. If you use Linnworks and Xero, SyncTools is a phenomenal tool, far superior to any alternative we've tried."
Deborah Whitfield
Customer
"I recently installed SyncTools and it is easy to use. The team worked quickly, kept me informed, and now everything runs smoothly."
Heather Cook
Customer
"Best Xero connector on the market. Excellent customer support and continuous development from an app that does exactly what it says."
Harvey Uppal
Customer
"AWESOME: Excellent tool and has saved us so much time. Credit to the support team for being so helpful in setup and post-setup."
Geoff Ainsworth
Customer
"Excellent tool: Does what it says and connects seamlessly & if you have any issues the support is amazing!"
Nirav Khiroya
Customer
"Fantastic support: The team has always been diligent and proactive about fixing any bugs that arise. Would highly recommend them."
Robert Morris
Customer
"Have been using the Linnworks Xero connector for a couple of years now. It is very reliable and the developers are keen to improve it."
Connie Sturman
Customer
"I just looked in the connector and it looks like they were able to get the purchase orders synced... thank the team for us. Thank you for your help."
Shopify QuickBooks Integration: Frequently Asked Questions
Common questions about connecting Shopify to QuickBooks Online with SyncTools
Does Shopify integrate with QuickBooks Online?
Yes. Shopify integrates with QuickBooks Online through SyncTools. The integration automatically syncs orders, refunds, fees, taxes, COGS, and Shopify payout settlements into QuickBooks as clean journal entries or individual transactions. You can categorize by country, product category, or sales channel. Setup takes under 15 minutes.
How does the Shopify to QuickBooks sync work?
SyncTools connects Shopify to QuickBooks Online via secure OAuth — no passwords stored. Once connected, every Shopify transaction is posted to QuickBooks within minutes. Choose summarized sync (daily journal entries) or individual transaction sync (one-to-one invoice/payment per order). All transactions map to your existing QuickBooks chart of accounts automatically.
What data syncs from Shopify to QuickBooks Online?
SyncTools syncs: sales orders, refunds, payment gateway fees (Shopify Payments, Stripe, PayPal), Shopify platform fees, shipping charges, sales tax by jurisdiction, cost of goods sold (COGS), and payout settlements. Each item is categorized by country/state, product category, or sales channel (Facebook, YouTube, POS, Online Store) and maps to the correct QuickBooks account.
How are Shopify refunds handled in QuickBooks?
Every Shopify refund is automatically posted to QuickBooks with the correct debit/credit entries. Refund amounts, associated fees, and restocked inventory are all accounted for. Partial refunds are supported. In summarized mode, refunds are netted into the daily journal entry; in individual mode, each refund creates a corresponding credit memo in QuickBooks.
How much does the Shopify QuickBooks Online integration cost?
SyncTools offers a free plan for up to 200 orders per month — no credit card required. Paid plans start at $19/month (Lite, up to 200 orders), with Standard at $59/month (2,000 orders/month) and Plus at $89/month (5,000 orders/month). All plans include the full Shopify QuickBooks integration.
Is SyncTools better than A2X or Synder for Shopify QuickBooks?
SyncTools, A2X, and Synder all offer Shopify QuickBooks Online integration. SyncTools is the only one with a free tier, offers the most granular categorization (by country, product, and sales channel), and includes phone/Zoom support on higher plans. The best tool depends on your reporting needs and order volume — SyncTools is strongest for merchants who need detailed breakdown and reconciliation.
Can I sync historical Shopify orders to QuickBooks?
Yes. When you first connect, select a historical backfill date range and SyncTools imports all past orders to QuickBooks. Available range depends on your plan: 3 months on Free/Lite, 6 months on Basic, 12 months on Standard/Plus. Historical sync uses the same categorization rules as live sync.
How does SyncTools handle multi-currency Shopify sales in QuickBooks?
SyncTools fully supports multi-currency. International Shopify orders are posted to QuickBooks in both the foreign currency and your QuickBooks base currency, using the exchange rate at time of transaction. This ensures accurate P&L reporting for UK, EU, and global merchants selling across multiple currencies.