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Recording PayPal and AfterPay Fees When Funds Are Received

Learn how to reconcile PayPal and AfterPay payments in your accounting package when fees are deducted before the funds reach your bank account.

Payment methods such as PayPal and AfterPay typically deduct their fees before paying out the balance to your dealership. This article explains how to handle the fee difference between what a customer pays in Blackpurl and what actually arrives in your bank account, so your accounting package stays reconciled correctly.

How It Works

When a customer pays a $100 invoice using PayPal, PayPal deducts its fee (for example, $5) and only deposits $95 into your bank account. Blackpurl records the full $100 payment, but your bank receives $95. The steps below explain how to account for that $5 gap in your accounting package.

Before You Start

Make sure both of the following are already configured:

  • PayPal or AfterPay is activated as a payment method in Blackpurl. See Selecting Payment Methods (no longer available) for details.

  • You have assigned an Undeposited Funds General Ledger for the relevant payment method under Accounting Integration > Undeposited Funds in Blackpurl. See Undeposited Funds General Ledger Explained for details.

When these are set up, any deposit or checkout taken in Blackpurl using PayPal or AfterPay is sent to your Undeposited Funds General Ledger in your accounting package, ready to be matched against your bank feed.

Step 1: Process the Payment in Blackpurl

Process the customer order as normal. When the customer pays a deposit or completes checkout using AfterPay or PayPal, select the relevant payment method at the time of payment.

Shows a payment interface with two main sections. On the left is a deposit dialog with 'Add deposit' button highlighted


The payment integrates to your accounting package and sits in the Undeposited Funds General Ledger you nominated under Accounting Integration > Undeposited Funds.

Step 2: Reconcile the Payment in Your Accounting Package

When the funds from PayPal or AfterPay arrive in your bank account, you need to allocate the bank transaction using two lines — one to clear the full amount from Undeposited Funds, and one to record the fee as an expense. Using the $100 PayPal example:

  1. Allocate $100 to the Undeposited Funds General Ledger. This clears the $100 that was recorded in Blackpurl.

  2. Add a second line for -$5 to your PayPal fees General Ledger (or whichever account you use to expense payment processing fees).

  3. Confirm the two lines net to $95 — matching the amount deposited in your bank account.

When done correctly, the bank allocation shows $95, which matches your bank deposit, and the $5 fee is recorded as an expense in the appropriate account.

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