Shopify Payments

If you're on Shopify, use Shopify Payments. The integration is seamless, fees are competitive, and using a third-party processor costs you an extra 0.5-2% in transaction fees.

On this page

When to Use Shopify Payments
Pricing Breakdown
What Shopify Payments Does Well
What Shopify Payments Does Poorly
Pricing Comparison (Shopify Plans)
- Break-Even Analysis
- Plan Recommendation by Volume
Who Shopify Payments Is Best For
- Perfect Fit
- Poor Fit
Common Gotchas
Test to Run
Scale Callouts
Where This Breaks
Shopify Payments vs Stripe (On Shopify)
Next Steps
See Also

When to Use Shopify Payments

You should use Shopify Payments if:

You're on Shopify (this is the default choice)
You want to avoid third-party transaction fees (0.5-2%)
You need faster payouts (next-day available)
You want unified reporting (sales + payments in one dashboard)
You're selling in multiple countries (supports 20+ countries)

Skip Shopify Payments if:

You're not on Shopify (it only works with Shopify)
You're in a high-risk industry (Shopify is conservative)
You need advanced fraud tools beyond Shopify's basic rules
You're processing outside Shopify's supported countries

Pricing Breakdown

Pricing by Shopify Plan

Shopify Payments rates depend on your Shopify plan tier:

Shopify Plan	Monthly Cost	Online Rate	Card-Present Rate	Transaction Fee (if using other gateway)
Starter	$5/month	3.3% + $0.30	N/A (online-only plan)	N/A
Basic	$39/month	2.9% + $0.30	2.7% + $0	2.0%
Shopify	$105/month	2.7% + $0.30	2.5% + $0	1.0%
Advanced	$399/month	2.4% + $0.30	2.4% + $0	0.5%
Plus	$2,300/month	2.15% + $0.30	2.15% + $0	0.15%

Key insight: Higher-tier plans have lower payment processing rates. Calculate the break-even point.

The Third-Party Penalty

If you use Stripe, PayPal, or another gateway instead of Shopify Payments, Shopify charges additional transaction fees:

Example on Basic plan ($39/month):

Shopify Payments: 2.9% + $0.30
Stripe through Shopify: 2.9% + $0.30 (Stripe) + 2.0% (Shopify fee) = 4.9% + $0.30

On $100K/month volume:

Shopify Payments: $3,200/month
Stripe on Shopify: $5,200/month
Extra cost: $2,000/month ($24,000/year)

This penalty makes third-party gateways uneconomical unless you have specific requirements Shopify Payments can't meet.

Hidden Costs

Fee	Amount	When It Applies
Shopify plan fee	$5-$2,300/month	Required to use Shopify Payments
Chargeback fee	$15	Win or lose
Currency conversion	1.5%	Multi-currency checkout
Manual payment	0%	Cash, check, bank transfer (no fee)
POS hardware	$49-$499	If doing card-present

Effective rate for most SMBs: 3.0-3.3% all-in for Basic plan merchants.

What Shopify Payments Does Well

1. Zero-Friction Integration

Shopify Payments is built into Shopify:

Enable in settings (no separate signup)
No API keys to manage
No webhook configuration
Instant activation for supported countries

Setup time: 5 minutes.

2. Unified Dashboard

All your data in one place:

Sales + payments + payouts
Chargeback management
Fraud analysis
Tax calculations
Customer management

Reality: You never leave the Shopify admin. This is worth something.

3. Faster Payouts

Shopify Payments offers faster access to funds:

Standard: 2-3 days
Daily payouts available (free)
Instant payouts: 1.5% fee (up to 3× daily limit)

Comparison: Stripe standard is 2 days, Square is 1-2 days.

4. Multi-Currency Checkout

Shopify Payments supports selling in 20+ countries:

Local payment methods
Local currency pricing
Unified reporting across currencies

Best for: International Shopify stores.

What Shopify Payments Does Poorly

1. Locked to Shopify Platform

You can only use Shopify Payments if you're on Shopify:

Leave Shopify = lose processor
Can't use for non-Shopify sales
No API for custom integrations

Platform lock-in risk: If you outgrow Shopify, you're migrating both store AND payment processor.

2. Limited Fraud Tools

Shopify's fraud detection is basic:

Simple rules (AVS, CVV, risk score)
No advanced ML-based screening
No device fingerprinting
Limited customization

Stripe Radar and dedicated fraud tools are better for high-fraud merchants.

3. Conservative Risk Tolerance

Shopify flags and holds accounts aggressively:

Sudden volume spikes = instant holds
High-ticket sales = payment delays
High chargeback ratio (>0.65%) = warnings

Common scenario: Launch a successful campaign, volume spikes 5x, Shopify freezes account for 1-3 days.

4. No Rate Negotiation Below Plus

Shopify Payments rates are non-negotiable until you're on Shopify Plus ($2,300/month):

Basic plan = 2.9% + $0.30 (no exceptions)
Shopify plan = 2.7% + $0.30 (no exceptions)
Advanced plan = 2.4% + $0.30 (no exceptions)

At $500K/month on Basic plan, you're paying $14,500/month with no negotiation option.

Pricing Comparison (Shopify Plans)

Break-Even Analysis

Should you upgrade Shopify plans for lower payment rates?

Example: $100K/month volume

Plan	Plan Cost	Payment Rate	Payment Fees	Total Cost
Basic	$39	2.9% + $0.30	$3,200	$3,239
Shopify	$105	2.7% + $0.30	$2,850	$2,955
Advanced	$399	2.4% + $0.30	$2,550	$2,949

Savings by upgrading Basic → Shopify: $284/month Savings by upgrading Shopify → Advanced: $6/month (not worth it until higher volume)

Break-even point:

Basic → Shopify: Worth it at $50K/month+
Shopify → Advanced: Worth it at $750K/month+

Plan Recommendation by Volume

Monthly Volume	Recommended Plan	Why
Under $25K	Starter ($5) or Basic ($39)	Minimize fixed costs
$25K-$200K	Basic ($39)	Best value, 2.9% + $0.30 is competitive
$200K-$750K	Shopify ($105)	0.2% savings = $400-$1,500/month
$750K+	Advanced ($399)	0.3% additional savings
$3M+	Plus ($2,300)	Custom rates, dedicated support

Who Shopify Payments Is Best For

Perfect Fit

Business Type	Why Shopify Payments Wins
Shopify stores	Seamless integration, avoid 3rd-party fees
Omnichannel	Shopify POS + online unified
International sellers	Multi-currency support
Print-on-demand	Integrated fulfillment + payments
Dropshipping	Lower barrier to entry

Poor Fit

Business Type	Better Alternative
High-fraud merchants	Stripe (better fraud tools)
Custom integrations	Stripe (better API)
Non-Shopify platforms	Can't use Shopify Payments
High-volume (>$1M/month)	Negotiate with Stripe or traditional processor

Common Gotchas

1. The Third-Party Transaction Fee Trap

Using Stripe instead of Shopify Payments on Basic plan:

Stripe fee: 2.9% + $0.30
Shopify transaction fee: +2.0%
Total: 4.9% + $0.30

On $100K/month: That's an extra $2,000/month ($24,000/year).

Never use a third-party gateway unless you have a very specific reason (e.g., Shopify Payments not available in your country).

2. Plan Tier Confusion

Merchants stay on Basic plan paying 2.9% when they should upgrade:

At $200K/month:

Basic: $39 + $5,800 fees = $5,839/month
Shopify: $105 + $5,250 fees = $5,355/month
Savings: $484/month ($5,808/year)

The $66/month plan upgrade pays for itself at $150K+/month.

3. Chargeback Threshold is Lower

Shopify Payments chargeback threshold is around 0.65%:

Over 0.65%: Warnings and account review
Over 1.0%: Account restrictions likely

This is lower than Stripe (0.75% threshold).

4. Account Holds on Spikes

Volume spike 3x+ in one month = automatic hold:

Funds frozen for 3-7 days while Shopify reviews
You can't prevent this, just expect it

Workaround: Email Shopify support before big launches to give them a heads-up.

Test to Run

Shopify plan optimization (if you're already on Shopify):

Week 1:

Pull last 3 months payment fees from Shopify analytics
Calculate average monthly volume
Calculate effective rate: total fees / total volume

Week 2: 4. Use break-even table above to check if you should upgrade plans 5. Calculate: (current fees) - (fees on next plan up) - (plan cost difference) 6. If savings > $0, upgrade

Week 3: 7. Check your chargeback ratio in Shopify → Analytics → Fraud 8. If over 0.5%, implement Chargeback Alerts

Success criteria: On the right Shopify plan for your volume, chargeback ratio under 0.5%.

Scale Callouts

Under $50K/month:

Basic plan is fine
2.9% + $0.30 is competitive
Don't overthink it

$50K-$250K/month:

Upgrade to Shopify plan ($105)
0.2% savings = $100-$500/month
Pays for itself immediately

$250K-$1M/month:

Consider Advanced plan ($399)
Savings are marginal unless over $750K
Evaluate if Shopify features justify staying vs migrating to Stripe

Over $1M/month:

Shopify Plus ($2,300) or migrate off Shopify entirely
Stripe with negotiated rates may be cheaper
Calculate migration costs vs long-term savings

Where This Breaks

Platform lock-in: If you outgrow Shopify and want to move to custom platform, you're migrating both store and processor. This is expensive and risky.
Limited customization: Shopify checkout is what it is. If you need custom payment flows, you'll struggle.
High-volume gets expensive: At $1M+/month, paying 2.4-2.9% with no negotiation means leaving $2K-$5K/month on the table vs negotiated rates.
High-risk rejection: Shopify is conservative. Supplements, CBD-adjacent, adult-adjacent = likely rejection.
Chargeback tools are basic: No advanced representment tools, no CE 3.0 automation. You're manually responding in the Shopify admin.