Reconciling Shopify Payments, Stripe & PayPal fees

Step-by-step guide to properly record gateway fees and reconcile payouts.

Gateway fees impact your profit margins. Here’s how to track them correctly in QuickBooks.

Why fee tracking matters

Payment processors take fees from each transaction:

• Shopify Payments: 2.9% + 30¢ per transaction
• Stripe: 2.9% + 30¢ (standard)
• PayPal: 2.9% + 30¢ (varies by volume)

If you only post gross sales to QuickBooks, your revenue is overstated and you can’t see true margins.

Correct accounting approach

Record:

1. Gross sales (full amount customer paid)
2. Gateway fees (expense)
3. Net deposit (what hits your bank)

Example:

• Customer pays: $100.00
• Gateway fee: $3.20 (2.9% + 30¢)
• Bank deposit: $96.80

QuickBooks entries:

• Revenue: $100.00
• Fee expense: $3.20
• Bank deposit: $96.80

Manual CSV method

Process:

1. Export orders from Shopify
2. Calculate fees manually (2.9% + 30¢ per transaction)
3. Post gross sales to revenue
4. Create separate expense entries for fees
5. Reconcile bank deposits

Problems:

• Time-consuming calculation for each order
• Easy to miss fee changes or special rates
• Refund fee handling is complex (partial fee credits)
• Must track multiple gateways separately

Gateway-specific differences

Shopify Payments

Fee structure:

• Transaction fee: 2.9% + 30¢
• Chargeback fee: $15 (non-refundable)
• Currency conversion: 1.5% additional

Payout timing:

• Daily payouts: arrives next business day
• Weekly/monthly: as configured

Fee on refunds:

• 2.9% is refunded, 30¢ is not
• Must track both fees separately

Stripe

Fee structure:

• Similar to Shopify Payments
• Volume discounts available
• Additional fees for international cards

Payout structure:

• Gross sales - fees = net payout
• Separate refund handling
• Balance transfers to bank

Reconciliation:

• Use Stripe balance transactions
• Match net payouts to bank

PayPal

Fee structure:

• Standard: 2.9% + 30¢
• Lower for nonprofits/volume sellers
• Higher for international transactions

Unique characteristics:

• Fees are non-refundable (even on refunds)
• Balance can stay in PayPal (not always to bank)
• Currency conversion fees

Accounting-grade app approach

Apps like Webgility and A2X handle fees automatically:

Webgility:

• Records gross sales to revenue
• Posts fees to expense account per gateway
• Creates bank deposit matching net payout
• Handles refund fee credits correctly
• Supports multiple gateways simultaneously

A2X:

• Specializes in payout reconciliation
• Matches QuickBooks entries to bank deposits
• Breaks out all fee types
• Settlement reports for accountants

Payout reconciliation workflow

Step 1: Understanding your payout

Shopify Payments payout includes:

• Gross sales from period
• Minus transaction fees
• Minus refunds (with partial fee credit)
• Minus chargebacks (with chargeback fee)
• = Net payout to bank

Step 2: QuickBooks posting

Create matching entries:

1. Revenue: All gross sales
2. Expenses: All fees broken out
3. Bank deposit: Net amount (must match bank)

Step 3: Reconciliation

• Open bank reconciliation in QuickBooks
• Match net deposit to bank feed
• If amounts match → reconcile ✓
• If mismatch → review fees and adjustments

Multi-gateway scenarios

If you use multiple gateways:

Separate expense accounts recommended:

• Shopify Payments Fees
• Stripe Fees
• PayPal Fees

Why:

• Track fee costs per gateway
• Compare gateway economics
• Optimize which gateway to promote

App advantage:

• Automatically routes fees to correct accounts
• No manual sorting needed

Common fee mistakes

❌ Posting net sales as revenue: Understates revenue ❌ Ignoring refund fee credits: Overstates expenses ❌ Missing chargeback fees: Hidden $15 costs ❌ Not tracking currency conversion fees: 1.5% adds up ❌ Lumping all fees together: Can’t optimize gateway choice

Refund fee handling

Full refund example:

• Original sale: $100, fee $3.20
• Refund: $100, fee credit $2.90 (30¢ not refunded)
• Net fee cost: $0.30

QuickBooks entries:

• Revenue credit: -$100
• Fee expense credit: -$2.90
• Net fee expense remains: $0.30

Manual tracking: Requires detailed refund analysis Apps: Handle automatically per gateway rules

Testing your setup

1. Single order test:

   • Process $100 test order
   • Check QuickBooks has $100 revenue + $3.20 fee
   • Verify bank deposit is $96.80

2. Refund test:

   • Refund the test order
   • Check revenue credit and partial fee credit
   • Verify remaining 30¢ fee expense

3. Payout reconciliation:

   • Wait for payout to arrive
   • Match QuickBooks deposit to bank amount
   • Reconcile successfully

When to use which method

Manual CSV:

• Only if <10 orders/month
• Single gateway
• No refunds

Zapier/Make:

• Not recommended (fee logic is complex)

Accounting-grade apps:

• 50+ orders/month
• Multiple gateways
• Refunds are common
• Need accurate margin reporting
• Want automated reconciliation

Bottom line

Gateway fees seem simple but get complex fast with refunds, multiple gateways, and currency conversion.

For clean books and true profit visibility, use an accounting-grade app that handles fee logic automatically. The time saved and accuracy gained pays for itself immediately.