Integration Guide
Shopify QuickBooks Online Connector
Integrate Shopify sales data with QuickBooks Online within minutes using SyncTools. Let's covert uncategorized Shopify sales payout data into organized summaries that reconcile seamlessly in QuickBooks Online. Try errorless accounting with Shopify QuickBooks Online integration.
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The Complete Toolkit for
Shopify x QuickBooks Accounting!
TL;DR: SyncTools connects Shopify to QuickBooks Online — automatically syncing sales, refunds, Shopify Payments fees, taxes, and payouts into the correct QuickBooks accounts every 30–45 minutes. Setup takes under 30 minutes with guided onboarding and no developer required.
- Automatically manage sales, purchases, refunds, expenses, fees, taxes & COGS.
- Categorize your Shopify sales at a granular level with channel-wise orders sync selection.
- Accelerate your accounting with the best Shopify QuickBooks integration.
- Also running WooCommerce? SyncTools covers WooCommerce QuickBooks integration too.
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Trusted by over 100+ great businesses
Two Ways to Sync Shopify with QuickBooks Choose What Fits Your Business
Summarised Sync to QuickBooks Journal Entries
With SyncTools, you can streamline your accounting by syncing summarised Shopify data directly into QuickBooks Online journal entries.
Instead of cluttering your books with thousands of individual transactions, SyncTools neatly consolidates your **sales, refunds, taxes, balances, and COGS **into a clean, accurate summary.
- Reduce data overload in QuickBooks with simplified journal entries
- Ensure accurate financial reporting by summarising sales, refunds, taxes, and COGS
- Save time and improve efficiency by automating Shopify to QuickBooks journal entry sync
- Perfect for multi-store, multi-region businesses needing clear financial insights
Take control of your Shopify accounting with a smarter, faster, and cleaner sync to QuickBooks Online.
Individual Transaction Sync to QuickBooks
SyncTools ensures every Shopify order, payment, product, customer, refund, fee, and COGS is synced individually into QuickBooks Online with perfect accuracy.
This one-to-one sync gives you a detailed, transparent view of your e-commerce accounting.
- One-to-one transaction mapping for complete accuracy
- Sync orders, payments, products, customers, refunds, fees, and COGS seamlessly
- Get real-time financial insights with every Shopify transaction in QuickBooks Online
- Ideal for businesses needing detailed transaction-level reporting
With SyncTools, your Shopify data flows effortlessly into QuickBooks, giving you the precision and depth needed for accurate financial management.
How to Connect Shopify to QuickBooks Online in 5 Steps
Connecting Shopify to QuickBooks with SyncTools takes under 20 minutes and requires no developer access.
Step 1 — Install SyncTools from the Shopify App Store Search for SyncTools and click Install. Grant permissions so SyncTools can read your Shopify orders, payouts, and transaction data.
Step 2 — Connect your QuickBooks Online account In SyncTools, go to Accounting System → QuickBooks Online. Complete the Intuit OAuth flow. SyncTools reads your chart of accounts and pre-fills a recommended account mapping.
Step 3 — Map Shopify transactions to QuickBooks accounts Assign each transaction type to the correct account: gross sales → Sales Revenue, Shopify fees → Merchant Fees, taxes → Sales Tax Payable (liability), refunds → Sales Returns, COGS → Cost of Goods Sold. A Shopify Clearing Account ensures the net payout matches your bank deposit exactly.
Step 4 — Choose summarized or individual sync Use summarized sync (daily journal entries) for high-volume stores or individual sync (one QuickBooks record per Shopify order) for granular reporting.
Step 5 — Run your first sync and reconcile Click Sync Now. In QuickBooks Banking, the Shopify payout deposit matches the SyncTools entry automatically — click Match and you’re done.
See also: How to record Shopify payout reconciliation in QuickBooks — a full walkthrough with chart of accounts.
Shopify accounting, stress-free!
SyncTools automates Shopify QuickBooks accounting for accurate books and easy reconciliation.
Auto-Categorize by Country and State
SyncTools saves you hours by automatically categorizing income and expenses not just by country, but also by state. This ensures highly accurate, detailed, and organized financial reports in QuickBooks Online.
- Simplify multi-region and multi-state accounting
- Gain deeper insights into profits and taxes by country and state
- Save hours on manual categorization and reporting
Take control of your global and regional finances with precision, and make better decisions with clear, structured reporting.
Know Which Products Drive Revenue
SyncTools streamlines your accounting by organizing income and expenses by product category, giving you deeper insights into which items drive your revenue.
- Understand your top performing categories.
- Organize your books by Shopify product attributes like type, category, tags, or collections.
- Easily create custom categories to suit your needs.
Track Revenue by Sales Channel
Effortlessly track your income and expenses by Shopify sales channels with SyncTools. Get a clear breakdown of where your revenue is coming from, all in one place.
- See performance across POS, Online Store, Meta, YouTube & more.
- Accurately track sales, fees, refunds as per channel.
Effortless Reconciliation, Maximum Accuracy
SyncTools automatically matches Shopify payout deposits with your bank statements, eliminating manual work and errors.
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100% accurate matching of payouts and deposits.
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Save hours on manual reconciliation.
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Ensure error–free, clean financial records.
Know Your True Profit
SyncTools consolidates your sales, refunds, shipping costs, and inventory valuations to give you a clear picture of your true net profit no guesswork, just accurate insights.
- Sync all revenue and expense details seamlessly.
- Track inventory value to ensure accurate calculations.
- Calculate true net profits with precise COGS data.
Deferred Revenue, Simplified!
SyncTools helps you handle deferred revenue effortlessly, ensuring income is recognized only when the related services or products are delivered.
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Automatically track unearned revenue.
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Stay compliant with IFRS 15 & ASC 606 automatically.
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Pay taxes only on recognized revenue, not total sales.
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Perfect for subscription based businesses revenue recorded when orders are fulfilled.
Set up in just 3 easy steps
1
Connect
2
Configure
3
Auto-Sync
Empower Your Business
with the Smartest Accounting Automation
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Save Time to Focus on Growth
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Clarity with True Profit Insights
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Payouts Synced, Reconciliation Done!
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Deferred Revenue, Simplified!
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Built for Multi Channel Accounting
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Data Security You Can Trust
How SyncTools elevates Shopify Commerce?
Increased efficiency
With the ability to sync sales, purchase, refunds, summarized sales, and COGS (cost of goods sold), your business can streamline its financial operations and reduce the time and effort required for manual data entry and reconciliation.
Improved accuracy
In eCommerce, manual data entry can result in errors, which can have significant financial consequences. By automating the process with your Shopify QuickBooks integration, you can improve the accuracy of your financial data and reduce the risk of errors.
Better financial insights
With your product’s capability to sync and summarize sales and COGS, you can gain a clearer understanding of your business’s financial performance and make data-driven decisions that can help drive growth.
Time and cost savings
Automating the Shopify to QuickBooks integration can save your business time and money by reducing the need for manual data entry and reconciliation. This can also free up your team’s time to focus on other important tasks.
Manage your bookkeeping effortlessly
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MonthlyYearlySave 12%
Free(Life-Time)
$0$0
USD/Month
USD/Year
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Upto **200 transactions/month**
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Lite
$19
$200
USD/Month
USD/Year
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Upto **200 transactions/month**
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Basic
$39
$412
USD/Month
USD/Year
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Upto **500 transactions/month**
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Standard
$59
$623
USD/Month
USD/Year
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Upto **2000 transactions/month**
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Plus
$89
$940
USD/Month
USD/Year
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Upto **5000 transactions/month**
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Add Ons
$ 5 per 100 additional transactions (for all plans)
$ 20 per business entity/months
More than 5000 orders?
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Compare plans and features
Usage
Free (Life-Time)
Lite
Basic
Standard
Plus
Monthly
$0 USD/Month
$19 USD/Month
$39 USD/Month
$59 USD/Month
$89 USD/Month
Yearly
$0 USD/Year
$200 USD/Year
$412 USD/Year
$623 USD/Year
$940 USD/Year
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Limits
Monthly Order Volume
Upto 200 transactions/month
Upto 200 transactions/monthy
Upto 500 transactions/month
Upto 2000 transactions/month
5000 transactions/month
Access to Historical Data
3 Months history
3 Months history
6 Months history
12 Months history
12 Months history
Supported Shopify Store
1 Store
1 Store
2 Stores
5 Stores
5 Stores
Linked QuickBooks Accounts
1
1
2
3
3
Additional Users Accounts
1
2
3
Unlimited
Unlimited
+
Features
Class and Location Mapping
COGS Synchronization
Monthly
Daily and monthly both
Daily and monthly both
Daily and monthly both
Tax Synchronization
Gift Card Synchronization
Default
Default
Default
Default
Default
+
Sales Data Grouping
By Payment Gateway
By Country
By Sales Channel
By Product Category
By Province/State
+
Summarized Sync
Mode
Manual
Manual & Auto
Manual & Auto
Manual & Auto
Manual & Auto
Frequency
Monthly
Daily, Weekly, Monthly
Daily, Weekly, Monthly
Daily, Weekly, Monthly
Daily, Weekly, Monthly
Send Sync Report via mail
Daily
Daily
Daily
Daily
Tax Threshold Notifications
Financial Summary by SyncTools
+
Individual Sync
Product, Customer, Sales
Tax, Refunds, Tips, COGS, Gift card
Categorisation based on Sales Channel
Payout and Fees
+
Other
Custom Development Services
Support
Email support, FAQs
Email support, FAQs
Phone Call, email support, FAQs
Phone Call, Zoom meeting, email support, FAQs
Phone Call, Zoom meeting, email support, FAQs
Want custom implementation in SyncTools-
Shopify QuickBooks connector?
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See how we compare
Evaluating alternatives before you commit? See how SyncTools stacks up:
- SyncTools vs A2X — detailed feature and pricing comparison
- SyncTools vs Synder — sync depth, multi-channel, and cost breakdown
FAQ: Shopify + QuickBooks integration
What is SyncTools?
SyncTools is an ecommerce accounting software that connects your Shopify store with QuickBooks Online. It automates the transfer of sales, refunds, taxes, and inventory data, helping you keep accurate financial records without manual effort.
Why should I integrate Shopify with QuickBooks using SyncTools?
SyncTools eliminates manual data entry, reduces accounting errors, and ensures real-time financial updates. This saves time, improves bookkeeping accuracy, and allows you to focus on growing your business.
How do I set up SyncTools for Shopify and QuickBooks Online?
Most Shopify merchants complete the SyncTools setup in 15 to 30 minutes. Install SyncTools from the Shopify App Store, connect your QuickBooks Online company via OAuth, and configure account mappings for sales, fees, refunds, taxes, and COGS. SyncTools pre-fills recommended account mappings based on your existing QuickBooks chart of accounts — review, adjust, and run your first sync.
Is SyncTools compatible with both QuickBooks Online and QuickBooks Desktop?
Currently, SyncTools is designed for QuickBooks Online. If you need integration with QuickBooks Desktop, please contact our support team for alternative solutions.
How does Shopify summarized sync work in SyncTools?
Summarized sync combines all transactions for a selected period (daily, weekly, or payout-wise) into a single summarized entry in QuickBooks. This simplifies bookkeeping by reducing the number of transactions recorded while maintaining accurate financial data.
When should I use summarized sync vs. individual sync in SyncTools?
Use Summarized Sync when you want to keep QuickBooks clean and reduce the number of transactions recorded. Ideal for merchants with high order volume.
Use Individual Sync when you need detailed transaction-level entries in QuickBooks for deeper financial tracking. Best for businesses that require granular reporting.
Can I connect multiple Shopify stores to one QuickBooks account using SyncTools?
Yes! SyncTools supports multi-store syncing, allowing you to connect multiple Shopify stores to a single QuickBooks account while maintaining separate financial tracking for each store.
Can I sync historical Shopify data to QuickBooks Online?
Yes, SyncTools allows you to import up to 24 months of historical data from Shopify to QuickBooks. You can choose the date range for syncing during setup. You will need to subscribe to the correct plan based on total historical order volume.
Can I customize how my Shopify data is synced with QuickBooks?
Yes, SyncTools offers flexible customization options, including mapping fields, choosing which data to sync, and setting sync frequencies to match your business needs.
How does SyncTools calculate Cost of Goods Sold (COGS)?
SyncTools automatically fetches product cost from Shopify orders and deducts them from each Shopify sale. This helps you understand your gross profit.
Can I customize the product costs for COGS calculations?
Yes! SyncTools allows you to overwrite the cost of product fetched from shopify, so that you can ensure that cost is inclusive of all types of costs related to procuring the product.
What should I do if I face any issues with the integration?
If you have any issues, you can check our Help Center, or documentation for quick solutions. For further assistance, follow these steps to contact our support team:
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Log in to your SyncTools account.
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Go to Get Support in the settings menu.
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Choose your preferred support option – Email or Phone.
Do you offer free support?
Yes! SyncTools provides free customer support to help with setup, troubleshooting, and optimizing your integration.
Is onboarding assistance included?
Yes! We offer a free onboarding to guide you through the setup process and ensure everything is configured correctly. This is limited to 4 hours.
Further Reading
- Shopify QuickBooks Integration Guide — step-by-step walkthrough of the full setup
- QuickBooks Automation for eCommerce — how to eliminate manual data entry and save hours monthly
- Shopify Sales Tax in QuickBooks — handling marketplace-collected tax so it never inflates your revenue
- Shopify Payout Reconciliation in QuickBooks — matching Shopify payouts to bank deposits with zero manual work
- eCommerce Sales Tax Compliance — economic nexus thresholds, marketplace facilitator rules, and how to stay compliant
- eCommerce Bookkeeping Fundamentals — chart of accounts setup and reconciliation principles every Shopify seller needs
Considering alternatives?
- SyncTools vs A2X — feature and pricing breakdown
- SyncTools vs Webgility — how SyncTools compares on accuracy, pricing, and support
- SyncTools vs Synder — side-by-side comparison for Shopify sellers
Ready to automate your accounting sync?
30-day free trial. No credit card required. All features included.