Payment processing costs are often underestimated when comparing WooCommerce and Shopify. The comparison isn't simple: WooCommerce has no platform fee but you pay plugin/gateway fees; Shopify charges platform fees but also offers its own payment processor (Shopify Payments) with no additional transaction fee. The right calculation depends on your revenue volume, location, and payment processor choice. Here's the full breakdown.

WooCommerce payment cost components

WooCommerce itself is free, but payment processing costs include:

Payment gateway plugin: WooCommerce Stripe, WooCommerce PayPal, etc. — typically free to install
Payment processor fees: Stripe standard rate (US): 2.9% + $0.30 per transaction. PayPal: 2.9–3.49% + $0.49 per transaction. Square: 2.6% + $0.10.
No WooCommerce/WordPress transaction fee on top of gateway fees (WooCommerce takes no cut)
Hosting: $20–$200/month depending on traffic (not payment-specific, but part of total cost)
SSL certificate: Required for payments. Free with Let's Encrypt or paid ($10–$200/year).
PCI compliance: With self-hosted WooCommerce, you bear PCI responsibility. Stripe's hosted payment fields (iframes) mitigate this but the store must maintain PCI DSS SAQ A-EP compliance.

Shopify payment cost components

Shopify plan subscription

Plan	Monthly	Annual (save ~25%)
Basic Shopify	$39	$29/mo ($348/yr)
Shopify	$105	$79/mo ($948/yr)
Advanced Shopify	$399	$299/mo ($3,588/yr)
Shopify Plus	From $2,300	Negotiated

Shopify Payments rates (US, 2025)

When using Shopify Payments (Shopify's built-in processor), there is NO additional transaction fee:

Plan	Online rate	In-person rate
Basic	2.9% + $0.30	2.6% + $0.10
Shopify	2.6% + $0.30	2.5% + $0.10
Advanced	2.4% + $0.30	2.4% + $0.10

Shopify Payments UK rates (2025):

Basic: 2.2% (no fixed fee)
Shopify: 1.9%
Advanced: 1.6%

Third-party gateway fees on Shopify

If using a payment processor OTHER than Shopify Payments (Stripe, PayPal, Square, Braintree), Shopify adds a transaction fee on top of the gateway fee:

Shopify plan	Transaction fee (third-party gateway)
Basic	2% per transaction
Shopify	1% per transaction
Advanced	0.5% per transaction
Shopify Plus	0.15%

This makes using third-party gateways significantly more expensive on Shopify. Example on Basic plan: Stripe 2.9% + 0.30 + Shopify 2% = effectively 4.9% + $0.30 per transaction.

Total cost modeling at $100,000/year revenue

WooCommerce with Stripe

Hosting (managed WooCommerce): $50/month = $600/year
Premium plugins: ~$300/year (theme, Yoast, security, etc.)
Stripe fees at 2.9% + $0.30 (assuming avg $50 order = 2000 transactions): 2.9% × $100,000 + 2000 × $0.30 = $2,900 + $600 = $3,500/year
Total: ~$4,400/year

Shopify Basic with Shopify Payments

Basic plan: $29/month annual = $348/year
No plugins needed for core functionality
Shopify Payments at 2.9% + $0.30 (2000 transactions): same $3,500/year
Apps for functionality WooCommerce plugins provide: ~$100–$300/year
Total: ~$4,148–$4,348/year (similar or slightly less)

Shopify (mid-tier) with Shopify Payments

Shopify plan: $79/month annual = $948/year
Shopify Payments at 2.6% + $0.30: 2.6% × $100,000 + 2000 × $0.30 = $2,600 + $600 = $3,200/year
Total: ~$4,148/year — comparable, with more built-in features

Where Shopify saves money

No hosting costs: WooCommerce hosting scales with traffic. High-traffic WooCommerce stores need $100–$500/month hosting. Shopify's plan includes hosting regardless of traffic.
No SSL costs: Included in all Shopify plans.
No plugin security updates: WooCommerce plugin maintenance time has a real cost — Shopify apps are maintained by vendors.
Faster checkout = higher conversion: Shop Pay's 15-20% higher conversion on cart abandonment and checkout can represent significant revenue at scale — harder to quantify but real.
No PCI DSS compliance burden: Shopify is PCI Level 1 certified. No SAQ required for stores using Shopify Payments.

Where WooCommerce can be cheaper

Very small stores: Under $20,000/year revenue — basic WooCommerce on cheap hosting ($5–$20/month) beats any Shopify plan cost.
Already have WordPress expertise: If managing WordPress/hosting in-house, the "labor cost" of WooCommerce plugins is zero.
High-volume EU stores using alternative gateways: Mollie, Adyen, or other EU gateways may offer lower rates than Shopify Payments in some EU markets. Using third-party gateways incurs Shopify transaction fees — at volume, this matters.
Custom payment flows: WooCommerce can support very custom checkout and payment flows that Shopify's checkout doesn't support (for most merchants this isn't relevant, but for some it is decisive).

Shopify Payments availability

Shopify Payments is available in:

United States, Canada, UK, Ireland, Australia, New Zealand
France, Germany, Netherlands, Belgium, Spain, Italy, Sweden, Denmark, Norway, Finland, Austria, Switzerland
Japan, Singapore, Hong Kong

In countries without Shopify Payments, third-party gateways incur the transaction fee. For stores in these markets, the math changes significantly — factor in the transaction fee when comparing to WooCommerce costs.

Payout schedules: WooCommerce vs Shopify

Processor	Payout timing
Stripe (WooCommerce)	2 business days (US), 7 days initially then rolling daily
PayPal (WooCommerce)	Instant to PayPal balance; bank transfer 1–3 days
Shopify Payments (US)	2 business days standard; 1 day with Shopify Balance
Shopify Payments (UK)	3 business days standard
Shopify Payments (AU)	2 business days standard

Chargebacks and disputes

Both Stripe (WooCommerce) and Shopify Payments have $15 chargeback fee
Shopify Payments provides chargeback management directly in admin (dispute evidence upload)
Stripe requires logging into Stripe dashboard for chargeback management

Payment cost migration checklist

Model total annual payment cost: plan + gateway fees + transaction fees (use actual annual GMV)
Check if Shopify Payments is available in your country — if yes, use it (eliminates transaction fee)
If Shopify Payments not available: factor in transaction fee (2% on Basic) in cost comparison
Compare hosting savings: what are you currently paying for WooCommerce hosting?
Calculate plugin cost savings: what plugin subscriptions are you replacing with Shopify native or free apps?
Enable Shopify Payments immediately after migration — don't use third-party gateway on Basic plan
Set up payout schedule in Shopify Payments settings
Ensure bank account details are correct for payouts before accepting live orders

For most stores above $50,000/year GMV with access to Shopify Payments, the total cost of ownership on Shopify (plan + processing) is comparable to or lower than WooCommerce when accounting for hosting, plugins, SSL, maintenance time, and security. The decision shouldn't be made on cost alone — but it's important to model it accurately rather than comparing the $39/month Shopify plan to "free WooCommerce" without the full picture.

Shopify payments fees vs WooCommerce: true payment cost comparison (2026)