Integrate Shopify with QuickBooks Online
Connect Shopify to QuickBooks Online with a Shopify QuickBooks integration that posts true FIFO COGS, landed cost, fee splits, and inventory journals — not revenue-only sync. NeonPanel completes the QuickBooks picture so margin matches cash.
Unified system
- Accounting
- Inventory
- Forecasting
- AI access
Trusted by 200+ ecommerce teams
What is missing from a native Shopify → QBO sync
Native Shopify → QuickBooks sync usually stops short of a defensible P&L:
- Sales figures arrive, but COGS are absent or estimated.
- Shopify fees and payment processing costs do not map to the right accounts.
- Inventory values in QuickBooks do not update when stock moves.
- If you also sell on Amazon, your books are split across two systems with no unified P&L.
Profit, not just revenue, in QuickBooks
How it works
Connect Your Accounts
OAuth Shopify and QuickBooks Online in a single setup flow.
Configure Your Mapping
Map sales, fees, tax, and refunds by collection, fulfillment, or region.
Automate & Sync
Orders, payouts, and COGS post on schedule; payout totals align with bank deposits for faster close.
One P&L, both channels
Running Shopify plus Amazon? NeonPanel rolls both into one QuickBooks Online P&L with channel-level classes or locations preserved.
See also: Amazon → QuickBooks, multi-warehouse inventory, forecasting and planning, or the ecommerce accounting hub.
Know your actual margin — not just your revenue
14-day free trial. No card required.
Start Free TrialSync Everything
Catalogs
Including Products, Services, Customers, Vendors, and Currencies
Charts of Accounts
Use the default Chart of Accounts tailored for Amazon sellers or customize your own
Bills
Bills, purchase orders, and expenses synced in real-time
Invoices
Precise Cost of Goods Sold (COGS) calculated using the First-In, First-Out (FIFO) method
Four channels for the same instrument layer
NeonPanel's structured ledger, batch-level COGS, and shipment-level inventory reach your team through MCP, Claude, Slack agents, or Viktor. Pick the surface that matches how you work.
Direct MCP
Build custom agents in Cursor, Claude Code, or your own stack against the NeonPanel MCP server.
Set up MCP → For analysts & operatorsClaude plugin
Eight specialist agents in Claude Code or Cowork — routing and MCP tools included.
Connect Claude → For teams in SlackAgents in Slack
@mention Dorian, Marta, Nina, and the full default roster directly in Slack — same agents as Claude.
Open Slack agents → General coworkerViktor in Slack
One @mention for routing — Viktor picks the domain when you prefer not to choose an agent.
Meet Viktor →Recommendations land on real FIFO batch costs, not industry averages.
Flexible Pricing Plans
Choose the plan that fits your business needs
Essentials
Includes 10,000 orders/month · additional orders billed separately
Perfect for growing businesses
- ✓ One Amazon Seller Account
- ✓ Flexible Landed Cost Distribution
- ✓ Automated COGS Calculations
- ✓ QuickBooks & Xero Integration
- ✓ Unlimited Users & Roles
Professional
Includes 10,000 orders/month · additional orders billed separately
For multi-entity & multi-warehouse operations
- ✓ All Essentials Features
- ✓ Custom Chart of Accounts
- ✓ Multi-Entity Accounting
- ✓ Multi-Warehouse Inventory
- ✓ FBA, AWD & ASDN Shipments
- ✓ Accounting & Logistics Agents
Frequently Asked Questions
Connect Shopify and QuickBooks Online to NeonPanel via OAuth, map sales, fees, tax, and refunds to your chart of accounts, then enable automated sync for orders, payouts, FIFO COGS, and inventory journals.
Sellers who need true SKU-level COGS and landed cost—not revenue-only connectors—use NeonPanel to complete the Shopify and QuickBooks integration with batch-level costing and multi-channel P&L in one ledger.
Yes. NeonPanel posts inventory movements, batch-level COGS, and fee splits into QuickBooks so gross margin reflects what you actually sold—not estimated averages from a basic connector.
NeonPanel syncs continuously on your configured schedule so sales, fees, and payouts stay current for reconciliation and month-end close.
Yes. NeonPanel can import and sync your historical Shopify transactions, ensuring your books are accurate and up-to-date from day one. You can specify the date range you want to import during setup.
Absolutely. You can connect as many Shopify accounts as you need to NeonPanel. All your accounts will sync to a single QuickBooks company, making it easy to manage multiple storefronts or marketplaces.