Reconcile PayPal in QuickBooks Online — Complete Fee Matching

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Reconcile Complete

QuickBooks Journal Entries Format
reconciled

Reconcile your PayPal account 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 PayPal Activity Download CSV

Download

How It Works

1

Export from PayPal

PayPal → Reports → Activity Download → Select 'Balance Affecting' → Download CSV

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 → PayPal account. Your balance should match.

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 Paypal Transactions fields map to Quickbooks Online Journal Entry

Paypal Transactions Source Value Quickbooks Online Journal Entry Target Value Note
Date 01/15/2025 → JournalDate 01/15/2025 Transaction date
Transaction ID 9AB12345CD678901E → JournalNo 9AB12345CD678901E Unique identifier for journal entry
Gross 100.00 → Credits 100.00 Gross amount credited to income
Fee -2.90 → Debits -2.90 Fee amount debited to expense
Net 97.10 → Debits 97.10 Net amount debited to PayPal bank account

Data Transformation

Each PayPal transaction splits into 2-3 journal lines

Input PayPal Transaction

Single row with Gross, Fee, Net amounts

Key columns: Date, Transaction ID, Gross, Fee, Net, Type
1:N — One input row creates multiple output rows
Output Journal Entry Lines 2-3 rows per input

Balanced debit/credit lines for double-entry

Why PayPal Reconciliation Is Challenging

The Gross vs Net Problem

PayPal shows you $100 received, but your bank shows $97.10 deposited. That $2.90 difference is PayPal's fee — but QuickBooks bank feeds only see $97.10. 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 PayPal transactions to proper Journal Entries that track everything: - Gross amount credited to Income (true revenue: $100) - Fee debited to Expense (tracked separately: $2.90) - Net debited to PayPal Bank (reconciles with bank: $97.10) Import these to QuickBooks, and your PayPal balance will match exactly. Fees are tracked as expenses. Revenue is accurate. Bank reconciles.

Common Journal Entry Import Errors

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

Pending Transactions Excluded

Only 'Completed' transactions are imported

Status: Pending, Held, Denied
Status: Completed

Filter PayPal export to balance-affecting transactions

Re-export from PayPal with 'Balance Affecting' filter

Mixed Currencies Detected

QBO Journal Entries use home currency only

Mixed USD, EUR, GBP transactions
USD transactions only (or single currency)

Export separate files per currency

Filter transactions by currency before import

Refund Signs Reversed

Refunds have negative Gross, positive Fee reversal

Gross: -100, Fee: +2.90, Net: -97.10
Correctly reversed journal entries

Processor handles sign reversal automatically

No action needed - handled by conversion

Why Use This Tool?

Complete Fee Tracking

Every PayPal 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

Payments, refunds, and transfers handled with correct accounting.

Month-End Close

PayPal balance in QBO matches PayPal dashboard when reconciled.

Audit Trail

Transaction IDs preserved for tracking back to PayPal.

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.
Not necessarily. You can use both — bank feed for quick reconciliation, and Journal Entries for proper fee tracking. Just be careful not to duplicate transactions.
After importing, your PayPal bank account balance in QuickBooks should match PayPal's 'Available Balance' in the dashboard. Any difference indicates missing transactions.
Withdrawals are recorded as transfers from PayPal to your bank account. They'll appear in both your PayPal register (negative) and your bank register (positive).
Most businesses reconcile monthly at month-end. Match your reconciliation period to your bank statement period for easier matching.
Some PayPal export settings exclude fees. Re-export from Activity Download and ensure all columns are included. Fee column should show negative values like -2.90.

Paypal → Quickbooks Online Data Ecosystem

All available data flows from Paypal to Quickbooks Online

Paypal Activity Download PayPal transaction history with payments, fees, refunds, and transfers
→
Quickbooks Online Journal Entry Double-entry accounting with debits/credits
Date → JournalDate Transaction ID → JournalNo Gross → Credits
Professional accounting, fee tracking, aggregated imports Current tool