QuickBooks sees Shopify revenue, not real profit
Shopify connectors move revenue; they rarely post true FIFO COGS, landed cost, fee splits, or inventory journals. 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
- COGS from actual batch costs. Landed cost allocated per unit, FIFO-calculated per sale.
- Fee mapping. Shopify transaction fees, payment gateway fees, and refunds mapped to the correct Chart of Accounts.
- Unified P&L. If you also sell on Amazon, NeonPanel combines both channels into one set of books.
- Real-time sync. Invoices, bills, inventory journals, and COGS entries push to QuickBooks automatically.
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
Three channels for the same instrument layer
NeonPanel's structured ledger, batch-level COGS, and shipment-level inventory are exposed to your AI through three channels. Pick the one that matches how your team works.
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
Connect NeonPanel to Claude Desktop in one click and ask questions about your real data in plain language.
Connect Claude → For founders & teamsViktor in Slack
Ask Viktor for FBA replenishment, profitability, and forecasting answers without leaving Slack.
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. Multiple Shopify accounts can feed one QuickBooks Online company with channel-level clarity for reporting.