Before You Begin
This guide is for E-commerce bookkeepers and advanced sellers. You’ll need detailed sales reports from Shopify and all connected payment gateways (e.g., PayPal, Sezzle).
Overview
What You’ll Learn
- How to identify and segment sales by each payment gateway
- Matching gross sales to specific payout reports from Shopify, PayPal, Sezzle, etc.
- Accurately accounting for all fees, refunds, and adjustments from each gateway
- Streamlining reconciliation for payouts that hit your bank account separately
1. Preparation Steps
Before diving into reconciliation, ensure your accounting software has these accounts:
Required Accounts (per gateway)
- Sales Income (e.g., Shopify Sales, PayPal Sales, Sezzle Sales)
- Payment Processing Fees (e.g., Shopify Fees, PayPal Fees, Sezzle Fees)
- Gateway Payout Bank/Asset Account (e.g., Shopify Payouts, PayPal Holding, Sezzle Holding)
- Sales Tax Payable (Liability)
Recommended for Granularity
- Refunds (Expense or Contra-Income)
- Discounts/Promotions (Income Reduction)
- Chargeback Expenses (Expense)
2. Understanding Payout Structures
Different payment gateways handle payouts in unique ways. It’s crucial to understand these differences for accurate reconciliation.
Shopify Payments Payouts
This is Shopify’s native gateway, typically handled by tools like A2X.
- Consolidated payout (sales, fees, refunds).
- Matches bank deposits directly.
- Easily automated with third-party tools.
- Requires setup for detailed breakdown.
- Needs careful mapping of line items.
- Can be confusing if mixed with other gateways.
External Gateway Payouts (e.g., PayPal, Sezzle)
These are payment methods processed outside of Shopify Payments.
Expert Tip: Each external gateway will send separate payouts to your bank. Treat each gateway as its own mini-bank account for reconciliation purposes, tracking its gross sales, fees, and net payouts independently.
- Individual payouts per gateway.
- Detailed transaction reports usually available.
- Directly reconcile bank deposits to specific gateway reports.
- Manual effort for segmentation.
- Can complicate overall sales reporting.
- Requires separate fee tracking per gateway.
3. Step-by-Step: Reconciling Multi-Gateway Payouts
The key is to account for gross sales and all deductions for each gateway before matching the net payout to your bank.
Here is a sample data structure you might expect from a gateway report.
{
"payout_id": "PX123456",
"gateway_name": "PayPal",
"payout_date": "2025-10-20",
"gross_sales_amount": 1500.75,
"transaction_fees": 45.02,
"refunds_issued": 50.00,
"net_payout_amount": 1405.73,
"transactions_included": [
{"order_id": "S12345", "amount": 100.00},
{"order_id": "S12346", "amount": 250.75}
]
}4. Implementation Guide
Let’s walk through the process for each payout type.
- 1
Generate Gateway Reports
Obtain detailed payout reports from Shopify Payments, PayPal, Sezzle, etc., covering the same period.
- 2
Record Gross Sales per Gateway
From Shopify’s sales reports, determine which orders were paid via Shopify Payments, PayPal, Sezzle, and record the gross sales for each.
- 3
Account for Fees & Deductions
For each gateway, post the fees, refunds, and other deductions to their respective expense/liability accounts. This should reconcile to the net payout.
- 4
Match Payouts to Bank Deposits
Once the gateway’s gross sales and deductions are recorded, the remaining net payout should precisely match the deposit in your bank account for that specific gateway.
Common Pitfall: Mixing Sales Data
Do NOT try to reconcile a PayPal deposit with your overall Shopify sales. Each gateway’s sales, fees, and payouts are distinct. Treat them separately to avoid reconciliation headaches.
5. Verification and Troubleshooting
Ensure your multi-gateway reconciliation is accurate and robust.
Reconciliation Checklist
- Gross sales from Shopify reports match sum of all gateway reports
- Each gateway’s net payout matches its corresponding bank deposit
- All fees (Shopify, PayPal, Sezzle, etc.) are accurately recorded as expenses
- Refunds and chargebacks are correctly applied against the relevant gateway
Need Help?
Expert Assistance
Struggling with complex multi-gateway reconciliations? Our specialist team can help simplify your bookkeeping.
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