Stale data = bad decisions. Summary journals hide the out-of-balance issues bookkeepers hunt at end-of-month.
Shopify accounting in QuickBooks Online must give you instant financial visibility.
weintegrate creates every sale as a real Sales Receipt / Invoice instantly with line-item accuracy to the penny and Shopify Payouts automatically reconciled as QuickBooks Online (QBO) bank deposits linked to real QBO documents — never batched summary journals. Balance Sheet, P&L, A/R, and inventory reports always current, not just after close.
Shopify App Store 
Core Features
Built Differently by Design, these fundamentals make weintegrate different
Instant Sync to QuickBooks Online (QBO)
Every Shopify order appears in QuickBooks Online instantly, not in batches at end of day or a week later — web or POS, B2C, B2B, or DTC, all fully supported. See accurate financials any time you need them and make informed decisions. Why instant sync matters more
Actual Transaction Documents
Each order creates a clear Sales Receipt / Refund Receipt or Invoice / Credit Memo transaction document in QuickBooks Online. No aggregated "Frankenstein" journal entries that hide what actually happened. Every order, a real transaction
Accurate
Transaction documents created in your QuickBooks Online accounting system that match your Shopify orders to the penny. No mystery discrepancies to chase down.
Customer Matching — Unique or Bulk (default catch-all)
Your business, your rules. Track every Shopify buyer as their own QuickBooks customer for full sales history and repeat-purchase visibility — or record every sale under one default catch-all customer (bulk) to keep your QuickBooks customer list clean. Switch any time. Both approaches are fully GAAP-compliant and work for any business model. New Customer Matching Advanced Rules
Item Matching — Unique or Bulk (default catch-all)
Map each Shopify product to its own QuickBooks item for line-item sales reporting — or record every sale against one default catch-all item per store (bulk) for frictionless bookkeeping without inventory overhead. When unique items are enabled and a product is configured as an inventory item in QBO, quantities are decremented automatically as orders sync. New Item Matching Advanced Rules
Operational Dashboard
Instant snapshot of your Shopify operations across every connected store — from a single screen. Five document views give instant visibility: Open Sales, Fulfilled Sales, Cancellations, Refunds, and Payouts — each with sync status indicators, quick filters, and daily and month-to-date totals. Know exactly where every order and payout stands without opening Shopify or QuickBooks. Trace any order in seconds
Sales Tax Handled Correctly
Per-order Sales Receipts and Invoices arrive in QuickBooks Online with line-item taxable flags, customer Bill-To and Ship-To addresses, the QBO Location, and the actual tax amount Shopify collected — recorded to the penny against the appropriate QBO tax agency. QBO's tax framework, driven by your tax-agency and nexus configuration (economic or physical), handles attribution and the Sales Tax Liability Report from there. No manual tax entry spreadsheets needed. Shopify sales tax in QBO
Automatic Reconciliation
Every Shopify payout is automatically reconciled to a real QuickBooks Online Deposit, with each linked transaction document — Sales Receipts and Refund Receipts, or Invoices, Payments, and Credit Memos for invoice-based accounting — posted as its own line. Processing fees, refunds, chargebacks, disputes, and the taxes Shopify collected each land in the right account, and any difference between the payout and the deposit is caught and flagged automatically, down to the penny. Automatic payout reconciliation
10-Minute Setup
Connect Shopify and QuickBooks Online in minutes, not hours. No complex mapping or configuration gymnastics required.
Built for Business Owners and Merchants, loved by Accountants and Bookkeepers
Instant and accurate visibility with GAAP-compliant design that makes month-end close actually pleasant
Audit-Friendly Records
Clear transaction history with Shopify orders (and their fulfillments, refunds, or cancellations) associated to QuickBooks Online transaction documents. Trace any sale in seconds. No aggregated journal entries hiding details making tracking down issues complex and lengthy. Balanced books vs correct books
GAAP principles from day one
No weird workarounds or "close enough" compromises. Built with GAAP principles from day one. Actual transaction documents in QuickBooks Online that match Shopify orders and Shopify payouts. GAAP from day one
Transaction-Level Detail
See every fee, discount, tax, shipping, and payment method broken out per order. No black-box aggregated summary numbers to reverse-engineer at month-end. Month-end without detective work
Payout to Deposit Report
Every Shopify payout generates a report linking each Sales Receipt and Refund Receipt to its QBO Deposit — with fees, chargebacks, and adjustments itemized. Discrepancies flagged instantly so month-end close takes minutes, not hours. The three-way payout report
Shopify Payout to QBO Deposit &
Discrepancy Report
Every Shopify payout generates a comprehensive report that links each transaction document to its QBO Deposit — and instantly flags any discrepancies, so you close the books with confidence.
- ✓ Automatic Linking: Sales Receipts and Refund Receipts (or Invoices and Credit Memos, depending on your sync configuration) automatically matched to each payout's QBO Deposit
- ✓ Discrepancy Detection: Instantly highlights any difference between the Shopify payout amount and the QBO Deposit amount
- ✓ Fee & Adjustment Breakdown: Processing fees, chargebacks, disputes, and credits itemized — no hunting inside QBO
- ✓ Single View: Side-by-side transaction counts, adjustment totals, and receipt summaries — no flipping between Shopify and QBO
What the Report Shows
- Side-by-side payout vs. QBO Deposit summary
- Linked Sales Receipts and Refund Receipts (or Invoices and Credit Memos) per transaction
- Discrepancy alerts with line-by-line problem details
- Shopify processing fees as deposit line details
- Credits, debits, chargebacks, and disputes itemized
- Transaction IDs, order numbers, amounts, and account associations
Advanced Capabilities
For complex businesses and growing operations
Multi-Store Support
Run multiple Shopify stores — web and POS, B2C and B2B, or separate brands? Each store gets its own sync configuration for clean separation in QuickBooks Online. Keep your accounting organized across every storefront without manual consolidation. One QBO company, B2C and B2B
Sync What Matters Skip What Doesn't
There are use cases where not every Shopify order belongs in QuickBooks. Set rules based on order tags, customer tags, fulfillment status, or payment gateway to control exactly what syncs to QuickBooks Online. Conditional sync rules
QuickBooks Class Assignment
Assign QuickBooks classes to items, shipping, discounts, and fees automatically. Get the granular P&L breakdowns your accountant needs — by brand, channel, location, or department. Every line sorted by class
Shipping as Line Item
Record Shopify shipping fees as a dedicated line item on every QBO Sales Receipt and Refund Receipt. Assign any Service-type QBO item to capture shipping revenue separately, with tax handling automatically matched to what Shopify charged. No shipping revenue buried in a catch-all field. Shipping fees on their own line
Live Fulfillment Tracking
When Shopify marks an order fulfilled, the QBO Sales Receipt or Invoice updates automatically — shipping date, tracking number, carrier (Ship via), and clickable tracking URL(s) embedded directly in the shipping line item. Every fulfillment detail lives inside QBO the moment an order ships, no copy-pasting between apps. Tracking on every shipped sale
Discount as Line Item
Track every Shopify discount as a dedicated line item on QBO transaction documents rather than a standard adjustment. Designate a Service-type QBO item for discounts, optionally assign a Class for departmental reporting, and get exact discount amounts synced with full audit-trail consistency at month-end. Discounts on their own line
Destination Fees & Surcharges
State-mandated retail delivery fees (e.g. Colorado, Minnesota) written as dedicated QBO line items — applied only when Shopify actually charges them. Retail Delivery Fee in QBO
Tips
Web and POS tips synced as a dedicated line item to any income account you designate — always tax-free, with optional Class assignment. Tips, their own income account
Payout Adjustment Tracking
Route each Shopify payout deduction to its own QBO account: Marketplace Sales Tax and Import Tax to liability accounts (pass-through funds remitted to tax authorities), Shipping Label Fees to an expense account, and Customs Duty to a dedicated liability account for cross-border compliance. Full visibility into every deduction — no lumping fees into a single catch-all. Every payout deduction, classified
What Gets Synced
Complete financial visibility from Shopify to QuickBooks Online
Orders
- ✓ Line items & totals
- ✓ Customer information
- ✓ Product SKUs and descriptions
- ✓ Discounts
- ✓ Shipping
- ✓ Tips
- ✓ Order notes and tags
- ✓ Fulfillment status with tracking number, carrier & date
Payments & Payouts
- ✓ Payment methods
- ✓ Gateway fees
- ✓ Payouts & QBO Deposits
- ✓ Refunds / Credit Memos
- ✓ Chargebacks & disputes
- ✓ Gift card transactions
Taxes
- ✓ United States sales tax — state, local & county
- ✓ Marketplace-collected sales tax
- ✓ Canada GST/HST, United Kingdom VAT, and Australia GST
- ✓ VAT, GST, IVA & TVA on the QBO Global edition
- ✓ Import tax & customs duty
- ✓ Tax exemptions
Fees & Adjustments
- ✓ Shopify & transaction fees
- ✓ Shipping label fees
- ✓ Destination surcharges, incl. Retail Delivery Fee
- ✓ Credits and adjustments
Your books, your level of detail — track customers and products individually in QuickBooks Online, or roll them into one default catch-all customer and item (bulk).
Either way, every total, tax, and payout still reconciles to the penny.
See All Features in Action
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