Reconcile Shopify Payments in QuickBooks — Complete Fee Matching

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Reconcile Complete

QuickBooks Journal Entries Format
valid rows

Reconcile your Shopify Payments in QuickBooks Online. Match Net amounts to bank, track fees as expenses, and close your books accurately.

No API required
Browser-based processing
Run on Google Cloud Platform

Download Sample

Sample Shopify Payout Transactions CSV

Download

Tool Rating

4.8 / 5 (512 votes)

How It Works

1

Export from Shopify

Settings → Payments → View payouts → Select payout → Export transactions

2

Convert to Journal Entries

Upload here, configure your QuickBooks account names

3

Import to QuickBooks

Settings → Import Data → Journal Entries → Upload converted file

4

Reconcile in QuickBooks

Go to Banking → Reconcile → Bank account. Your balance should match.

Why Shopify Reconciliation Is Challenging

The Gross vs Net Problem

You sold $1,000 on Shopify, but your bank shows $970 deposited. That $30 difference is Shopify's processing fee — but QuickBooks bank feeds only see $970. Without proper handling, you either understate revenue (recording only Net) or your books won't reconcile with your bank (recording Gross).

How This Tool Helps

We convert Shopify transactions to proper Journal Entries that track everything: - Gross amount credited to Income (true revenue: $1,000) - Fee debited to Expense (tracked separately: $30) - Net debited to Bank (reconciles with bank: $970) Import these to QuickBooks, and your Shopify balance will match exactly. Fees are tracked as expenses. Revenue is accurate. Bank reconciles.

Your Data is Safe

Bank-Level Security

256-bit SSL encryption. Same standards as major financial institutions.

No Data Storage

Files are processed directly in browser. No calls to our servers.

GDPR Compliant

Full EU data protection compliance. Your privacy rights protected.

ISO/IEC 27001 Certified GDPR Compliant Swiss Privacy CCPA Compliant

Field Mapping

How Shopify Transactions fields map to Quickbooks Online Journal Entry

Shopify Transactions Source Value Quickbooks Online Journal Entry Target Value Note
Date 2025-01-15 → JournalDate 01/15/2025 Transaction date to MM/DD/YYYY
Amount 100.00 → Credits 100.00 Gross sales credited to revenue
Fees 2.90 → Debits 2.90 Processing fees debited to expense

Why Use This Tool?

Complete Fee Tracking

Every Shopify processing fee recorded as a separate expense line item.

Bank Reconciliation Ready

Net amounts match your bank feed exactly. Reconcile in minutes.

Revenue Accuracy

Gross amounts recorded as income. See your true revenue, not net.

Transaction Type Handling

Charges, refunds, disputes, and adjustments handled with correct accounting.

Month-End Close

Shopify balance in QBO matches Shopify dashboard when reconciled.

Audit Trail

Order numbers preserved for tracking back to Shopify.

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Data Transformation

Transactions aggregated by payout, then each payout expands to 3-7 JE lines

Input Shopify Balance Transactions

Multiple transactions per payout (charges, refunds, fees, disputes)

Key columns: Amount, Fee, Net, Type, Payout ID
N:M — Complex transformation
Output Journal Entry Lines 3-7 rows per input

Double-entry accounting separating gross sales, fees, and net deposit

DR Bank Deposit DEBIT bank: net amount that hit your bank
DR Processing Fees DEBIT expense: Shopify/payment processing fees
CR Gross Sales CREDIT income: gross sales revenue (matches 1099-K)
DR Refunds DEBIT income: reduce revenue for refunds
DR Disputes DEBIT income: chargebacks reduce revenue
DR Dispute Fees DEBIT expense: $15 chargeback fee per dispute
Debits must equal Credits (Bank + Fees = Gross - Refunds - Disputes)

Common Journal Entry Import Errors

Issues you might encounter when importing Payouts/Transactions data to Journal Entry - and how we solve them

Unbalanced Journal Entry

QuickBooks requires Debits = Credits for each journal entry

Debit: $970, Credit: $1000 (unbalanced)
Debit: $970 + $30, Credit: $1000 (balanced)

We auto-calculate balanced entries: Bank + Fees = Sales

Each payout creates a balanced entry with fee breakdown

Account Names Not Found

QuickBooks import fails if account names don't match your Chart of Accounts

Account: 'Shopify Sales' (not in your QB)
Account: 'Sales Income' (matches your QB)

Configure your actual account names before converting

Use the account settings to match your QuickBooks Chart of Accounts

Duplicate Journal Number

Importing the same payout twice creates duplicate entries

Payout #12345 imported twice
Each payout ID is unique

Journal numbers include payout ID to prevent duplicates

Check your date range to avoid re-importing processed payouts

Bank Deposit Doesn't Match

Your bank shows $970 but you recorded $1000 in sales

$1000 sales recorded, $970 bank deposit (where's $30?)
$1000 sales - $30 fees = $970 bank deposit

Journal entries separate gross sales from processing fees

Fees are tracked separately so bank reconciliation works

Frequently Asked Questions

Journal Entries allow proper split accounting (Gross to income, Fee to expense, Net to bank). Bank transaction imports only accept single amounts and can't properly track fees.
Enable 'Use Clearing Account' to credit a clearing account instead of sales. This prevents double-counting revenue while still recording fees and reconciling bank deposits.
After importing, your bank account balance in QuickBooks should match your actual bank statement. Any difference indicates missing transactions or duplicate entries.
Disputes are tracked separately as losses when 'Track Disputes Separately' is enabled. This gives you clear visibility into chargeback costs including the $15 dispute fee.
Most businesses reconcile monthly at month-end. Match your reconciliation period to your bank statement period for easier matching.
Make sure you're exporting the Payout Transactions (not just Orders). The Fee column should show amounts like $2.90 for each transaction.

Shopify → Quickbooks Online Data Ecosystem

All available data flows from Shopify to Quickbooks Online

Shopify Customers Export Customer profiles with contact info, addresses, and marketing preferences
→
Quickbooks Online Customer Import Customer profiles with contact and billing information
First Name → First Name Last Name → Last Name Email → Email
Customer list migration, CRM sync
Shopify Orders Export Customer orders with line items, shipping, taxes, discounts, addresses
→
Quickbooks Online Invoice Accrual-basis B2B sales (payment pending)
Name → InvoiceNo Created at → InvoiceDate Created at → DueDate
Wholesale, net terms, accounts receivable
Shopify Orders Export Customer orders with line items, shipping, taxes, discounts, addresses
→
Quickbooks Online Sales Receipt Cash-basis B2C sales (payment received at checkout)
Name → RefNumber Created at → TxnDate Billing Name → Customer
Retail, e-commerce, paid orders
Shopify Payouts/Transactions Shopify Payments transactions, fees, and bank deposits
→
Quickbooks Online Journal Entry Double-entry accounting with debits/credits
Date → JournalDate Amount → Credits Fees → Debits
Professional accounting, fee tracking, aggregated imports Current tool
Shopify Products Export Product catalog with variants, pricing, inventory, and images
→
Quickbooks Online Products and Services Import Product and service items for invoicing and sales
Title → Name Variant SKU → SKU Variant Price → Sales Price/Rate
Product catalog migration, inventory setup
Shopify Refunds (via Orders Export) Refunded orders filtered from Orders export. Filter by Financial Status = refunded.
→
Quickbooks Online Journal Entry Double-entry accounting with debits/credits
Created at → JournalDate Name → JournalNo Refunded Amount → Debits
Professional accounting, fee tracking, aggregated imports
Shopify Tax Summary Report Sales tax collected by jurisdiction for liability posting
→
Quickbooks Online Journal Entry Double-entry accounting with debits/credits
Period End → JournalDate Tax Jurisdiction → Account Name Tax Collected → Credits
Professional accounting, fee tracking, aggregated imports