WooCommerce Payments to QuickBooks: Fee Reconciliation & Journal Entry Tool

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Convert Complete

QuickBooks Journal Entries Format
valid rows

Reconcile WooCommerce Payments deposits with fees in QuickBooks for accurate accounting

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

Download Sample Orders

Example WooCommerce paid orders

Download Sample

Tool Rating

4.9 / 5 (67 votes)

How It Works

1

Export WooCommerce Orders

Export completed orders from WooCommerce (paid orders only)

2

Configure Fee Rates

Enter your payment gateway's fee structure (percentage + fixed amount)

3

Upload & Generate

Upload order CSV and download journal entry file

4

Import to QuickBooks

Go to Gear > Import Data > Journal Entries and upload the file

5

Reconcile Bank

Bank deposits now match journal entry amounts for easy reconciliation

The WooCommerce Payments Net Deposit Problem

Net vs Gross Accounting Issue

The Problem: - WooCommerce shows $100 order total (gross) - Stripe/WooCommerce Payments deposits $95.50 to your bank (net after $4.50 fee) - Bank statement shows $95.50 - QuickBooks needs to show $100 sales revenue AND $4.50 expense Without proper reconciliation, your books won't match your bank, or you'll underreport revenue.

The Solution: Journal Entries

Create balanced journal entries for each deposit: - DEBIT Bank Account: $95.50 (matches bank statement) - DEBIT Payment Fees: $4.50 (expense account) - CREDIT Sales Revenue: $100.00 (gross sales) This shows true revenue ($100) while matching your bank ($95.50).

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 Woocommerce Orders fields map to Quickbooks Online Journal Entry

Woocommerce Orders Source Value Quickbooks Online Journal Entry Target Value Note
order_total 155.50 → Credit: Sales Revenue Gross sale amount
order_date 2024-01-15 14:30:00 → Date Transaction date

Why Use This Tool?

Fee Calculation

Calculates Stripe/WooCommerce Payments fees automatically (2.9% + $0.30)

Balanced Entries

Creates perfectly balanced journal entries (debits = credits)

Bank Reconciliation

Journal entry amounts match your bank statement deposits exactly

True Revenue Tracking

Records gross sales in revenue account while tracking fees separately

Customizable Fee Rates

Configure for different payment gateways (Stripe, PayPal, WooCommerce Payments)

Expense Account Setup

Properly categorizes payment fees as operating expenses

Data Transformation

Each order becomes 3 balanced journal entry lines (Bank DR, Fees DR, Sales CR)

Input Order with Fee Data

One row per order with gross, fee, and net amounts

Key columns: order_total, payment_fee, net_deposit
1:N — One input row creates multiple output rows
Output Journal Entry Lines 3 rows per input

3 lines per order (double-entry balanced)

DR Bank Deposit DEBIT bank account for net amount received
DR Payment Fees DEBIT expense account for processing fees
CR Gross Sales CREDIT revenue account for gross sales
Debits (Bank + Fees) must equal Credits (Sales) for balanced entry

Common Journal Entry Import Errors

Issues you might encounter when importing Orders Export data to Journal Entry - and how we solve them

Journal Entry Doesn't Balance

Debits must equal Credits in double-entry accounting

DR Bank $95.50, DR Fees $4.50, CR Sales $99.00 (imbalanced)
DR Bank $95.50, DR Fees $4.50, CR Sales $100.00 (balanced)

Ensure gross = net + fees; tool validates balance before export

Check WooCommerce export includes accurate fee data

Payment Fee Data Missing

WooCommerce order export doesn't include payment gateway fees

Order export has total but no fee breakdown
Need separate WooCommerce Payments payout report

Export WooCommerce Payments > Deposits report or Stripe balance transactions

Combine order export with payout report, or estimate fees (e.g., 2.9% + $0.30)

Frequently Asked Questions

Recording only net deposits ($95.50) understates your true revenue ($100). You need to show gross sales for accurate financial reporting, profit margins, and tax reporting. Payment fees should be categorized as operating expenses, not revenue reductions.
Yes! Just enter the correct fee rates. PayPal is typically 2.9% + $0.30 (same as Stripe). WooCommerce Payments uses Stripe's rates. For other gateways, check their fee schedule and update the percentage and fixed fee settings.
The tool can estimate fees based on standard rates (2.9% + $0.30), or you can export a payout report from Stripe/WooCommerce Payments that shows actual fees and net amounts for each transaction.
Match your bank statement frequency. If you have daily deposits, create journal entries daily. For weekly/monthly payouts, batch your orders and create one journal entry per payout matching the bank deposit.
A2X ($19-149/month) automates this process with real-time sync. Our tool is perfect if you don't need real-time updates and want to avoid monthly fees. Process your deposits weekly or monthly at a fraction of the cost.

Woocommerce → Quickbooks Online Data Ecosystem

All available data flows from Woocommerce to Quickbooks Online

Woocommerce Customers Export WooCommerce customer/user data (one row per customer)
→
Quickbooks Online Customer Import Customer profiles with contact and billing information
first_name + last_name → Name company → Company email → Email
Customer list migration, CRM sync
Woocommerce Orders Export WooCommerce order data with line items (one row per product)
→
Quickbooks Online Invoice Accrual-basis B2B sales (payment pending)
order_number → InvoiceNo billing_first_name + billing_last_name → Customer order_date → InvoiceDate
Wholesale, net terms, accounts receivable
Woocommerce Orders Export WooCommerce order data with line items (one row per product)
→
Quickbooks Online Journal Entry Double-entry accounting with debits/credits
order_total → Credit: Sales Revenue payment_fee → Debit: Payment Fees net_deposit → Debit: Bank Account
Professional accounting, fee tracking, aggregated imports Current tool
Woocommerce Products Export WooCommerce product catalog data (one row per product)
→
Quickbooks Online Products and Services Import Product and service items for invoicing and sales
Name → Name SKU → SKU Regular price → Sales Price/Rate
Product catalog migration, inventory setup