Your Shopify dashboard says you made $50,000 this month. You check your bank account: $42,000 deposited.
Where did $8,000 go?
This is one of the most common confusions for Shopify merchants. The short answer: Shopify shows gross sales, your bank shows net deposits after fees, refunds, and timing delays.
This guide breaks down every factor so you can reconcile the numbers—and understand your actual cash flow.
Understanding the Gap
Shopify Dashboard = Gross Sales
What customers paid at checkout
Bank Deposit = Net After Deductions
What you actually receive
The difference typically breaks down like this:
| Deduction | Typical % | On $50K Gross |
|---|---|---|
| Payment processing fees | 2.4-2.9% | $1,200-1,450 |
| Shopify subscription | Fixed | $79-399 |
| Transaction fees (if not Shopify Payments) | 0.5-2% | $250-1,000 |
| Refunds | 2-5% | $1,000-2,500 |
| Chargebacks | 0.5-1% | $250-500 |
| Timing (pending payouts) | Variable | $500-3,000 |
| Total gap | 8-16% | $4,000-8,000 |
Fee Breakdown
Every credit card transaction has a processing fee:
- Shopify Payments: 2.4-2.9% + $0.30 per transaction (varies by plan)
- Third-party gateway: Gateway fee + Shopify transaction fee (0.5-2%)
- PayPal: 2.9% + $0.30 (+ Shopify transaction fee if applicable)
Example: On a $100 order with Shopify Payments on Basic plan (2.9% + $0.30), you pay $3.20 in processing fees. Your deposit: $96.80.
Your monthly plan fee is deducted from payouts:
- Basic: $39/month
- Shopify: $105/month
- Advanced: $399/month
- Plus: $2,000+/month
Some apps charge percentage fees deducted from payouts:
- Shop Pay Installments fees
- Certain shipping apps
- Some marketing/upsell apps
Timing Differences
Shopify records sales immediately. Bank deposits are delayed:
- Standard: 2 business days after order
- New accounts: May have longer holds (up to 14 days)
- High-risk flags: Reserves may be held
Sales on Jan 30-31 may not deposit until Feb 2-3. If you're comparing monthly revenue to monthly deposits, timing creates gaps.
Go to Settings → Payments → View payouts to see pending amounts and payout schedule.
Refunds & Chargebacks
- Full refund: Entire order amount deducted from future payout
- Partial refund: Partial amount deducted
- Note: You don't get processing fees back on refunds
Example: Customer orders $100, you pay $3.20 processing, they return it. You refund $100, lose the $3.20 processing fee. Net impact: -$3.20
When customers dispute charges:
- Full order amount held/deducted
- Chargeback fee ($15-25 typically)
- If you win dispute, funds returned (but not always the fee)
A 1% chargeback rate on $50K = $500 in disputed orders plus $75-125 in fees.
Other Factors
If you sell in multiple currencies:
- Shopify shows amounts in customer's currency
- Bank receives your base currency after conversion
- Conversion fees (1.5-2%) apply
Gift card sales show as revenue but aren't "earned" until redeemed. This can create accounting confusion.
Shopify may show gross sales before discounts in some reports. Check if you're looking at "Gross sales" vs. "Net sales."
How to Reconcile
- Shopify: Analytics → Reports → Finances → Payments
- Look at "Total payouts" not "Total sales"
- Bank: Total deposits from Shopify Payments
- Add pending payouts to bank total
- Or compare on a lag (this month's deposits ≈ last month's sales)
| Item | Where to Find | Add/Subtract |
|---|---|---|
| Gross sales | Shopify Analytics | Starting point |
| Payment processing fees | Finances → Payments | Subtract |
| Refunds issued | Finances → Payments | Subtract |
| Chargebacks | Finances → Payments | Subtract |
| Pending payouts | Settings → Payments | Note (timing) |
| Shopify subscription | Settings → Billing | Subtract |
| = Net to bank | Result |
If numbers still don't match within 1-2%, contact Shopify support with specific transaction IDs.
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Key Takeaways
- Shopify shows gross sales; bank shows net after fees, refunds, and timing
- Payment processing fees (2.4-2.9%) are the biggest deduction
- Timing differences can create 5-10% monthly variance
- Refunds cost you the order amount PLUS the original processing fee
- Use Shopify's Payments reports (not Sales reports) for accurate reconciliation