How to Connect Shopify to QuickBooks: Step-by-Step

Before you connect Shopify to QuickBooks Online (or Desktop), take 20 minutes to get your accounts in order. Skipping this step is the single biggest cause of messy data and failed reconciliations later.

1. Confirm your QuickBooks edition is ready. If you are using QuickBooks Online (QBO), make sure you are on at least the Essentials plan -- the Simple Start plan lacks purchase orders and multi-currency support. If you are on QuickBooks Desktop, confirm your version is 2022 or newer; older versions have deprecated API support that breaks most connectors.

2. Set up your Chart of Accounts. At a minimum, create or verify these accounts before installing any integration:

• Shopify Sales -- Revenue (Income account)
• Shipping Income -- Revenue for shipping charges collected
• Payment Processing Fees -- Expense account for Shopify Payments, PayPal, and Stripe fees
• Shopify Clearing Account -- Other Current Asset, used to hold payout amounts before they hit your bank
• Discounts Given -- Contra-revenue or Expense account
• Refunds Issued -- mapped back to Revenue as a credit, or a separate contra-revenue account
• Cost of Goods Sold (COGS) -- Direct Costs, if you track product costs

3. Verify Shopify admin access. You need the Store Owner or a Staff account with full permissions. A staff account with limited access will not be able to authorise the OAuth connection required by integration apps.

4. Know your payment gateways. List every payment method active on your Shopify store: Shopify Payments, PayPal, Stripe, Klarna, manual payments, gift cards. Each gateway deposits funds independently, so each one needs its own clearing account in QuickBooks. Miss one, and your reconciliation will never balance.

5. Decide on your inventory method. If you sell physical products, decide now whether QuickBooks or Shopify will be your inventory source of truth. For most e-commerce businesses, Shopify manages physical stock levels (quantities, reorder points, warehouse locations) while QuickBooks tracks the financial value (COGS on the profit and loss, inventory asset on the balance sheet). Do not try to sync stock quantities bidirectionally -- it creates conflicts and data overwrites.

The simplest way to link Shopify to QuickBooks is through the official connector available in the Shopify App Store. This connector is developed and maintained by OneSaaS (an Intuit company), not by Shopify. It is free to install and use, which makes it the default starting point for many merchants.

The connector imports sales data from Shopify into QuickBooks Online as invoices or sales receipts. It groups transactions by day and payment method, mapping them to accounts you configure during setup.

Follow these steps to install and configure the official Intuit connector:

1. Install from the Shopify App Store. Search for "QuickBooks Online" or "Intuit QuickBooks Connector" in the Shopify App Store. Click Install and authorise the app to access your Shopify store data.
2. Connect your QuickBooks Online account. The app opens a standard Intuit OAuth flow. Sign in with your QuickBooks credentials and select the correct company file. If you manage multiple QBO companies, double-check you are connecting to the right one.
3. Map your accounts. The connector asks you to map Shopify data to QuickBooks accounts: revenue, shipping, discounts, tax, and fees. Use the accounts you set up in the pre-integration checklist. Pay particular attention to tax codes -- incorrect tax mapping causes VAT reporting errors that are tedious to unravel.
4. Set your sync preferences. Choose whether to import orders as Sales Receipts or Invoices. For most B2C stores, Sales Receipts are correct (payment is collected at checkout). If you sell B2B with net terms, use Invoices instead.
5. Run an initial sync. The connector allows you to import historical data -- typically the last 30 to 90 days. Start with a small date range (one week), verify the data in QuickBooks, then backfill further if needed.
6. Activate automatic syncing. Once your test data looks correct, enable daily automatic sync. Data typically updates within two hours of a sync trigger.

The official connector handles the following data:

• Orders (as Sales Receipts or Invoices) grouped by day
• Refunds (as Credit Memos or Refund Receipts)
• Products synced as items in QuickBooks (name and SKU must match)
• Tax amounts mapped to your configured tax codes
• Customer records (optional -- can create customers in QBO or map all sales to a single "Shopify Customer")

It does not sync real-time inventory quantities, purchase orders, or cost of goods sold journals. Payment processing fees are also not broken out automatically -- they arrive as part of the net payout, which means your revenue figure will be understated if you do not account for fees separately.

The free Intuit Connector works for basic setups, but it has significant limitations that affect accuracy and scalability:

• No fee breakdown: Payment processing fees (typically 2.9% + EUR 0.30 per transaction) are not recorded as a separate expense. You must manually calculate and post fees, or accept that your revenue figures are net of fees rather than gross.
• SKU matching is strict: Product SKUs in Shopify must match QuickBooks item names or SKUs exactly. A single character difference -- an extra space, a different case, a missing hyphen -- causes the sync to fail for that product, and the transaction may be skipped entirely without a clear error message.
• Limited multi-currency support: The connector struggles with stores that sell in multiple currencies. Currency conversion is handled at the payment gateway level, and the connector does not always pass the correct exchange rate to QuickBooks.
• Daily summary only: Individual order-level detail is not preserved in QuickBooks. You get a summary per day per payment method, which makes it difficult to trace a specific customer complaint or refund back to its original order.

For stores processing more than 50 orders per month, the free connector's limitations become painful quickly. Payout summary tools solve the core problem: they match your QuickBooks entries to your actual bank deposits, making reconciliation seamless.

Instead of posting individual orders or daily summaries, these tools create one journal entry or invoice per Shopify payout. Since each payout corresponds to a single bank deposit, matching in QuickBooks is a one-click operation.

The workflow is straightforward:

1. The tool reads your Shopify payouts (the actual bank deposits Shopify sends you)
2. For each payout, it breaks down the components: gross sales, shipping collected, discounts, refunds, payment processing fees, Shopify transaction fees, and the net deposit amount
3. It creates a summary entry in QuickBooks that maps each component to the correct account
4. When the payout arrives in your bank feed, you match it against the clearing account entry -- the amounts should match exactly

This approach means your QuickBooks figures are always reconcilable to the penny. Every bank deposit has a corresponding entry that breaks down exactly what it contains.

Here is an independent comparison of the three leading payout summary tools for Shopify QuickBooks integration as of early 2026:

Which should you choose?

• A2X (EUR 19--99/month) is the gold standard for e-commerce accountants. Its per-payout summaries are audit-ready, and it handles multi-channel (Amazon + Shopify + eBay) under one subscription. If your accountant recommends a tool, it will almost certainly be A2X.
• LinkMyBooks (EUR 17--65/month) offers nearly identical functionality at a lower price point. Rated 4.9/5 in the Shopify App Store, it is the best-value option for stores that need proper payout reconciliation without the premium pricing.
• Synder (EUR 20--200/month) stands apart because it can sync individual orders (not just payout summaries) into QuickBooks. This is useful if you need per-order detail in your accounting system, but it creates significantly more transactions in QuickBooks, which can slow down reporting for high-volume stores.

Payout summary tools handle accounting data accurately, but they stop at the QuickBooks door. Full automation platforms go further: they manage inventory sync, order-level detail, COGS tracking, multi-channel consolidation, and intelligent reconciliation in a single workflow.

Full automation platforms like Webgility and FinTask cover capabilities that payout summary tools do not:

• Order-level posting with fee separation: Every Shopify order is posted to QuickBooks with gross revenue, fees, tax, and discounts broken out as separate line items -- not lumped into a payout summary. This gives you full audit trails without sacrificing reconciliation accuracy.
• Inventory synchronisation: Product quantities, costs, and SKU mappings stay in sync between Shopify and QuickBooks. When an order ships, COGS is automatically calculated and posted. When you receive new stock, the inventory asset account updates accordingly.
• Multi-channel consolidation: If you sell on Shopify, Amazon, eBay, and your own website, a full automation platform consolidates all channels into a single QuickBooks workflow. No more juggling four separate integration apps.
• Intelligent exception handling: FinTask applies AI to flag anomalies -- unexpected fee spikes, duplicate transactions, SKU mismatches, and reconciliation discrepancies -- before they snowball into month-end problems.

Webgility starts at EUR 49/month for a single channel and scales to EUR 249/month for multi-channel, high-volume plans. It has been in the market since 2007 and has deep QuickBooks Desktop integration -- making it the top choice for merchants who still run Desktop rather than QBO.

FinTask takes a different approach. Rather than replacing your existing integration tool, FinTask sits on top of your Shopify-to-QuickBooks data flow and applies AI-powered automation to the tasks that still require human judgement: reconciliation matching, intelligent categorisation of edge cases, anomaly detection, and real-time reporting. Whether you use the free Intuit Connector, A2X, or Webgility to move data into QuickBooks, FinTask ensures that data is correct, categorised, and reconciled without manual intervention.

For businesses processing 200+ orders per month across multiple channels, full automation pays for itself within the first month by eliminating 10--20 hours of manual bookkeeping and reconciliation work.

While QuickBooks Online dominates the cloud accounting market, many established businesses still run QuickBooks Desktop (Pro, Premier, or Enterprise). Connecting Shopify to QuickBooks Desktop requires a different approach because Desktop does not have a native web API -- it uses a local sync agent instead.

How the Desktop connector works:

1. Install the sync agent. The integration provider (Webgility, OneSaaS, or a similar tool) installs a small desktop application on the same machine that runs QuickBooks Desktop. This agent acts as a bridge between the cloud-based Shopify data and your local QuickBooks company file.
2. Configure the sync scheduler. Set the agent to sync at regular intervals -- typically every 1--4 hours during business hours. The agent pulls new Shopify orders and posts them to your QuickBooks Desktop company file as Sales Receipts, Invoices, or Sales Orders.
3. Map accounts and items. The same account mapping process applies: revenue, fees, shipping, discounts, and tax codes must be mapped to the correct QuickBooks Desktop accounts. SKUs must match exactly between Shopify and QuickBooks Desktop item lists.
4. Keep QuickBooks Desktop running. The sync agent can only write to the company file when QuickBooks Desktop is open and the file is not in single-user mode (unless the agent supports QuickBooks Desktop's "Auto Data Recovery" or background sync features). If someone closes QuickBooks Desktop, the sync queue builds up until the application is reopened.

Desktop-specific considerations:

• Webgility is the market leader for Shopify-to-QuickBooks Desktop integration. It offers the deepest Desktop feature set, including inventory sync, COGS posting, and multi-location support.
• Firewall and network: The sync agent needs outbound internet access to reach Shopify's API. Corporate firewalls sometimes block this -- whitelist the agent's endpoints during setup.
• Version compatibility: QuickBooks Desktop 2022 and newer are fully supported. Older versions (2019--2021) work with most tools but may lack certain API features. Versions before 2019 are no longer supported by Intuit and should be upgraded.
• Data updates arrive within approximately two hours of the scheduled sync, assuming QuickBooks Desktop is running and the company file is accessible.

Choosing the right method to connect Shopify to QuickBooks depends on your order volume, number of sales channels, and how much accounting detail you need. Use this decision matrix:

Key takeaway: The free Intuit Connector is a reasonable starting point for stores with fewer than 50 orders per month. Once you exceed that threshold, the time you spend manually reconciling fees, tracking down SKU mismatches, and fixing tax mapping errors costs more than a EUR 19/month payout summary tool. For multi-channel or high-volume operations, full automation is not a luxury -- it is a necessity.

After setting up your Shopify QuickBooks integration, do not assume everything is working. Run these verification checks within the first week:

Check sales data accuracy. Compare Shopify's Sales by channel report (Analytics > Reports > Sales) against the revenue figures in QuickBooks for the same date range. The gross sales figure should match. If it does not, check whether payment processing fees are being deducted from revenue (they should not be -- fees belong in an expense account, not netted against income).

Verify inventory values. If your integration syncs COGS, pull a Shopify product export and compare the cost prices against the item costs in QuickBooks. Discrepancies here mean your COGS calculations will be wrong, which directly affects your gross margin reporting. SKUs must match exactly -- this is the most common source of inventory sync failures.

Test reconciliation end-to-end. Wait for a Shopify payout to arrive in your bank feed, then try to reconcile it in QuickBooks:

1. Open your bank feed in QuickBooks and find the Shopify (or Stripe) deposit
2. Match it against the corresponding entry in your Shopify clearing account
3. Verify the formula: Gross Sales - Fees - Refunds - Discounts = Net Payout
4. If the figures match, reconcile. If they do not, check the integration app's sync log for errors or skipped transactions

Run a test refund. Process a small test refund in Shopify and confirm it appears correctly in QuickBooks -- typically as a Credit Memo or Refund Receipt that reduces revenue and adjusts the clearing account balance. Refund handling is where many integrations break down, especially when partial refunds or restocking fees are involved.

Even well-configured integrations encounter issues. Here are the most common problems when connecting Shopify to QuickBooks and how to resolve them:

Transactions not syncing. The first thing to check is your OAuth connection. QuickBooks Online tokens expire periodically, and a disconnected token silently stops all syncing. Open your integration app's settings and re-authorise the QuickBooks connection. If you are on QuickBooks Desktop, confirm that the sync agent is running and that QuickBooks Desktop is open with the correct company file loaded.

Duplicate transactions. Duplicates occur when you switch integration tools without properly closing out the old one, or when sync date ranges overlap during setup. To fix: identify and delete the duplicate entries in QuickBooks, then adjust the sync start date in your integration app so it picks up exactly where the old sync left off. Never run two integration apps simultaneously -- they will both post the same transactions.

SKU mismatches. When a Shopify product's SKU does not match any item in QuickBooks, the integration either skips the transaction, posts it to a generic "uncategorised" account, or fails entirely -- depending on the tool. The fix is straightforward but tedious: export your Shopify product list, export your QuickBooks item list, and compare SKUs character by character. Common culprits include trailing spaces, uppercase versus lowercase letters, and hyphens versus underscores.

Payout amounts do not match. If the bank deposit does not match the clearing account balance in QuickBooks, the issue is almost always one of these:

• Missing fees: Payment processing fees were not recorded separately, so the clearing account shows the gross amount but the bank received the net amount
• Timing: A refund was processed after the payout was calculated but before it settled, so it is included in the next payout rather than this one
• Multi-currency conversion: The exchange rate applied by Shopify Payments differs from the rate QuickBooks used, creating a small variance (typically under EUR 2). Post these differences to a Currency Gains/Losses account
• Shopify transaction fees: If you use a third-party payment gateway alongside Shopify Payments, Shopify charges an additional transaction fee (0.5--2%) that some connectors do not capture

Tax mapping errors. If the wrong tax rate is assigned to Shopify sales, your VAT returns will be incorrect. Review the tax code mapping in your integration app's settings. For EU sellers operating under the One Stop Shop (OSS) scheme, ensure each country's VAT rate is mapped to a separate QuickBooks tax code. The free Intuit Connector does not handle multi-country VAT well -- this is a strong reason to upgrade to a paid tool if you sell across EU member states.

Answers to the most common questions about Shopify QuickBooks integration.

Connecting Shopify to QuickBooks is the foundation of accurate e-commerce accounting. Whether you choose the free Intuit Connector, a payout summary tool like A2X or LinkMyBooks, or a full automation platform, the goal is the same: get your sales data into QuickBooks automatically so you can stop re-typing numbers and start making decisions based on real-time financial data.

But moving data into QuickBooks is only half the job. You still need to reconcile payouts, catch errors, categorise edge cases, and close your books on time. That is where FinTask comes in.

FinTask sits on top of your Shopify-to-QuickBooks integration and applies AI-powered automation to the work that still requires human judgement:

• Automated reconciliation: Payouts are matched to clearing account entries automatically, with mismatches flagged before you open QuickBooks
• Intelligent categorisation: Unusual transactions, new fee types, and one-off charges are categorised based on your historical patterns
• Anomaly detection: Fee spikes, duplicate entries, and SKU mismatches are caught in real time -- not during month-end close

Connect Shopify to QuickBooks with FinTask and turn your e-commerce data flow into a genuinely hands-off accounting process. Or explore the Full QuickBooks Integration Guide to see how FinTask works across your entire accounting stack.

Already using Shopify with another accounting platform? See our guides for Shopify Xero Integration and Stripe QuickBooks Integration. Or visit the Shopify Integrations hub for a complete overview of every Shopify accounting connector.