Introduction

The best shopify payment app gives you faster payouts, lower fees, higher conversion rates, and fewer disputes. Choosing the right payment stack can add 1 to 5 percentage points to conversion and save thousands in fees as order volume grows.

This guide explains which payment apps to consider, how to compare fees and features, and a practical 30-60-90 day rollout plan. You will get clear vendor comparisons (Shopify Payments, Stripe, PayPal, Adyen, Klarna, Affirm, Square), fee examples, integrations for subscriptions and buy now pay later (BNPL), and a checklist to avoid common pitfalls. Read this when you are launching a store, expanding internationally, or reworking checkout to improve margin and conversion.

What this covers and

why it matters:

payment provider choices affect checkout speed, accepted payment methods, fraud risk, affordability of returns, multi-currency support, and marketing options like Shop Pay installments. Make choices based on real metrics: transaction fees, payout timing, dispute rates, and customer friction.

Best Shopify Payment App Options

Selecting the best shopify payment app depends on your priorities: lowest variable fees, fastest payouts, best conversion on mobile, global currency coverage, or financing options. Below are the most common, with typical pricing and when to use each.

Shopify Payments (Shopify Inc.)

Typical US online card rate: 2.9% + $0.30 on Basic plan, 2.6% + $0.30 on Shopify plan, 2.4% + $0.30 on Advanced plan. Fees vary by country and plan.
Payouts: 2 business days in many markets; varies by country.
Best when: you want the simplest integration, auto-activated fraud protection, Shop Pay (accelerated checkout) and unified dashboard for refunds and payouts.

Stripe

Typical rate: 2.9% + $0.30 per successful card charge in US; volume discounts possible.
Strengths: global reach, multi-currency, excellent developer tools, many Shopify apps integrate natively (subscriptions, marketplaces).
Best when: you need advanced customization, marketplace routing, or non-Shopify storefronts.

PayPal (PayPal Commerce Platform)

Typical rate: 2.9% + $0.30 for US transactions; PayPal Express/Checkout can lift conversion among PayPal users.
Strengths: buyer trust, widely used, easy guest checkout.
Best when: your customers are older demographics or you want to accept PayPal/PayPal Credit.

Adyen

Pricing: custom enterprise pricing; usually competitive at scale.
Strengths: enterprise-level global acquiring, local payment methods (WeChat Pay, UnionPay), good for high international volumes.
Best when: you have cross-border volume and need local acquiring and reporting.

BNPL options (Klarna, Affirm, Afterpay/Clearpay)

Merchant fees: typically 2-6% + fixed fee depending on market and merchant risk.
Strengths: increases AOV (average order value) and conversion on higher-ticket items.
Best when: average order value is above $150 and you want to reduce checkout friction for financing.

Square and Worldpay

Strengths: unified POS and online payments (Square), broad acquiring networks (Worldpay).
Best when: you operate physical retail plus ecommerce and want single reconciliation.

How to read the fee numbers: for a $100 order, a 2.9% + $0.30 fee equals $3.20. For a BNPL fee of 4% on $300, merchant cost is $12. Example: switching from 2.9% to 2.4% saves $0.50 on a $100 order, scaling to $500 savings per 1,000 orders.

Actionable tip: list your top 3 priorities (fees, payouts, BNPL, global support) and score each provider 1-5. Use that score to narrow to 2 finalists before testing.

How to Choose the Right Payment App

Choosing means balancing cost, conversion, and operational risk. Use these decision criteria and a scoring matrix to pick the best shopify payment app for your store.

Step 1 - Define priorities (example weights)

Conversion impact: 30 percent
Fee structure and total cost: 30 percent
Settlement timing and cash flow: 15 percent
Fraud and dispute management: 15 percent
Integration and reporting: 10 percent

Step 2 - Gather provider data points

Effective fee: include interchange plus, fixed fee, gateway fee, and monthly fees. Example: Stripe 2.9% + $0.30 vs Shopify Payments 2.9% + $0.30 - similar headline costs, but Shopify Payments eliminates third-party gateway fees if used in Shopify.
Chargeback fee: usually $15 to $25. Add the expected chargeback rate (0.2% average) to expected costs.
Payout cadence: daily, 2 days, or 7+ days. Faster payouts reduce working capital needs.
Currency support: multi-currency settlement avoids conversion fees.
Buyer experience: does the provider support Shop Pay, Apple Pay, Google Pay, and one-click repeat purchases?

Step 3 - Build a simple cost model (example)

Monthly orders: 2,000
Average order value (AOV): $60
Monthly GMV (gross merchandise value): $120,000
Effective fee difference: 0.5 percent between Provider A and B -> $600 monthly savings.

Step 4 - Scorecard template (use a simple spreadsheet)

Rows: providers
Columns: conversion score (1-5), fee cost ($), payout days, dispute handling score (1-5), multi-currency (yes/no).
Weight and compute a total score to rank providers.

Risk and compliance considerations

PCI DSS (Payment Card Industry Data Security Standard): Shopify Payments and hosted gateways reduce your PCI scope.
Data residency and GDPR: For EU customers, check where payment provider stores data.
KYC (Know Your Customer) requirements: some providers require merchant documentation at signup and may restrict industries.

Actionable example: If you sell internationally with AOV $200 and 30 percent revenue from EU, prioritize multi-currency and local acquiring. Score Adyen and Stripe higher; keep Shopify Payments if it supports the key currencies.

Implementing Payments:

step-by-step 30-60-90 day plan

A structured rollout reduces risk and lets you measure lift. Below is a 30-60-90 day plan to deploy and optimize the best shopify payment app for your store.

Days 0-30: Selection and setup

Finalize provider using the scoring model and negotiate pricing if possible.
Create test accounts and enable sandbox mode for Stripe, PayPal sandbox, or Shopify test payments.
Configure payment methods: credit cards, Apple Pay, Google Pay, Shop Pay, PayPal, BNPL.
Checklist:
Enable HTTPS on storefront.
Confirm currency settings and tax behavior.
Add business legal documents for KYC.
Test flows: guest checkout, returning customer, refund and partial refund, subscription trial (if relevant).

Days 31-60: Pilot and monitor

Run A/B test for checkout flows: current vs new payment mix. Primary KPI: conversion rate; secondary KPI: average order value and completed checkout rate.
Track metrics daily: GMV, transactions, chargebacks, refunds, payout timing.
Validate reconciliation: confirm payouts match dashboard and bank deposits.
Implement fraud rules: set velocity limits, AVS (address verification) thresholds, and card verification value (CVV) masks. Consider Signifyd or Riskified if fraud is significant.

Days 61-90: Scale and optimize

Roll out to 100% of traffic if pilot shows positive results or comparable results with cost savings.
Add payment features: BNPL for high-ticket items, localized methods for target countries, saved cards for one-click checkout.
Negotiate rates: present 60-day volume to payments rep and request tiered discounts.
Establish SOPs (standard operating procedures) for disputes, refunds, and reconciliation.

Example timeline numbers

A/B test: run for 2 weeks or 5,000 visitors minimum to reach statistical relevance.
Expected conversion lift from Shop Pay or BNPL: 2-20 percent depending on audience and AOV.
Typical time to full payout normalization: 1-2 payout cycles (7-14 days) to validate settlement cadence.

Actionable tip: keep a payments runbook with contact info for gateway support, merchant ID, PSP (payment service provider) rep, and dispute escalation steps.

Optimizing Checkout and Revenue with Payment Features

Payment choices influence conversion, average order value, and operational cost. Focus on features that reduce friction and increase wallet variety.

Accelerated checkout

Offer Shop Pay, Apple Pay, and Google Pay. These reduce form fields and speed payment on mobile, improving conversion by 10-30 percent for mobile-heavy stores.
Example: if mobile conversion is 1.5 percent and you add Apple Pay leading to 20 percent relative lift, conversion becomes 1.8 percent. For 50,000 monthly visitors at $60 AOV, that is ~150 extra orders or $9,000 monthly incremental GMV.

Buy Now Pay Later (BNPL)

Add Klarna, Afterpay/Clearpay, or Affirm for orders above $150 to raise AOV and conversion.
Example impact: retailers report AOV increases of 30-60 percent for orders that use BNPL.
Monitor cost: BNPL merchant fees can be 3-6 percent; ensure margin supports adoption.

Saved cards and subscriptions

Use Stripe or Shopify Payments to enable saved card tokens and recurring billing.
For subscriptions, use ReCharge or Shopify Subscriptions. Example fees: ReCharge has monthly plans starting near $60 plus transaction fees; Shopify has native subscription APIs with different cost structures.

Fraud and risk management

Turn on machine learning fraud filtering: Shopify Payments and Stripe Radar reduce fraud rates. Consider third-party protection for high-value or fraud-prone niches.
Example: a 0.5 percent fraudulent order rate on $100k monthly GMV equals $500 lost plus chargeback fees; better fraud controls can cut that loss by 50 percent or more.

Payment messaging and trust signals

Display accepted logos (Visa, Mastercard, Shop Pay) and offer a secure checkout badge.
Add estimated processing time and refund policy to checkout to reduce abandonment.

Actionable A/B tests

Test one-click checkout vs standard checkout for returning users.
Test BNPL on product pages vs only on checkout to measure discovery lift.
Measure time-to-payment and abandonment points using heatmaps and funnel analytics.

Tools and Resources

Below are common tools, typical pricing, and why you would use them. Pricing is indicative; negotiate for volume.

Payment gateways and processors

Shopify Payments
Pricing: variable by plan (example US: Basic 2.9% + $0.30; Shopify 2.6% + $0.30; Advanced 2.4% + $0.30).
Availability: global; country-specific support.
Use: simple setup, Shop Pay, integrated payouts.
Stripe
Pricing: typical 2.9% + $0.30 in US; volume discounts.
Use: customization, subscriptions, marketplaces, global cards.
PayPal Commerce Platform
Pricing: 2.9% + $0.30 (US); PayPal Express checkout widely used.
Use: trusted brand and guest payments.
Adyen
Pricing: custom enterprise pricing.
Use: cross-border acquiring, local payment methods.

BNPL providers

Klarna
Merchant fees: typically 2-6% depending on region and product.
Use: increases AOV and conversions on larger orders.
Afterpay / Clearpay
Fees: merchant percentage + fixed fees; varies by country.
Use: retail and fashion verticals.

Subscription apps

Recharge
Pricing: starts around $60/month plus transaction fees.
Use: subscription box and recurring revenue models.
Shopify Subscriptions (native)
Pricing varies; built into Shopify ecosystem with applied usage fees.
Use: native integration and lower maintenance.

Fraud protection

Stripe Radar (included options) and Radar for Fraud Teams (paid).
Signifyd
Pricing: percent of revenue or per-transaction; often $0.50-$1.00 per order or percentage-based.
Use: chargeback guarantee and automation.

Analytics and reconciliation

A2X (for accounting)
Pricing: from $19/month.
Use: automates payouts and transaction-level reconciliation for Shopify + Stripe/PayPal.

Developer and integration tools

Webhooks and APIs from Stripe and Shopify to automate refunds and reconcile charges.
Zapier for light automations if you lack engineering resources.

Actionable selection tip: start with providers that reduce your operational overhead. For example, Shopify Payments removes a gateway fee and integrates with Shop Pay; it is often the fastest path to a clean reconciliation.

Common Mistakes and How to Avoid Them

Choosing only on headline rates

Mistake: picking the provider with the lowest headline percent without considering fixed fees, chargeback costs, and cross-border FX.
How to avoid: model effective fees at your current order mix and estimate chargebacks and refunds for 6-12 months.

Ignoring mobile payment options

Mistake: not enabling Apple Pay, Google Pay, or Shop Pay, which increases form friction on mobile.
How to avoid: enable accelerated payment methods and test mobile funnel. Expect 10-30 percent mobile conversion lift.

Not testing payouts and reconciliation

Mistake: assuming dashboard numbers match bank deposits.
How to avoid: reconcile first 2-3 payout cycles and document mismatches; set up A2X or manual SOP.

Overlooking fraud rules and chargeback process

Mistake: reactive dispute handling leading to higher chargeback losses.
How to avoid: implement automated fraud scoring, require CVV/AVS on suspicious orders, and create a chargeback playbook.

Failing to display local payment methods

Mistake: only offering cards in markets that favor local wallets (e.g., Klarna in Nordics, iDEAL in Netherlands).
How to avoid: research top payment methods by country and enable them where you advertise.

FAQ

What is the Single Best Shopify Payment App for a Small US Store?

For most small US stores, Shopify Payments is the simplest and most cost-effective option because it integrates with Shop Pay, removes third-party gateway fees, and offers competitive rates. Add PayPal for conversion lift among PayPal users.

How Much Can BNPL Increase My Average Order Value?

Buy now pay later options commonly increase average order value by 20-60 percent depending on product price and audience. Track AOV for BNPL users versus non-BNPL users over 30 days to quantify impact.

Are International Cards Accepted by Shopify Payments?

Yes, Shopify Payments accepts international cards in supported countries and offers multi-currency settings. For complex global acquiring or local payment methods, consider Stripe or Adyen.

How Do Chargeback Fees Work and How Can I Reduce Them?

Chargeback fees are fixed fees (often $15-$25) plus the lost order amount if not won. Reduce them by improving fraud detection, requiring verification on suspicious orders, clear shipping/tracking, and rapid response with evidence.

Do I Need a Separate Gateway If I Use Shopify Payments?

No, Shopify Payments acts as both gateway and processor in supported countries, removing the need for a separate gateway and usually saving gateway fees. For certain payment methods (Adyen, international acquiring), a separate provider may still be needed.

How Quickly Will I Get Paid After a Sale?

Payout timing varies: Shopify Payments and Stripe commonly settle in 1-3 business days in many markets; PayPal balances are immediate in-platform but bank withdrawals take 1-3 days. New accounts may have longer holds for risk reasons.

Next Steps

Build your scoring sheet

Create a simple spreadsheet with providers, weights, and expected monthly cost model based on your order volume and AOV. Use it to pick 2 finalists.

Run a 30-day pilot

Enable chosen providers in test mode, route a portion of traffic or run an A/B test, and collect conversion, refund, and payout data.

Implement fraud and reconciliation SOPs

Set up automatic alerts, a payout reconciliation checklist, and an escalation path for chargebacks. Assign a single owner for payments operations.

Optimize and negotiate

After 60-90 days of volume, present data to providers and negotiate better rates or exclusive features. Add BNPL or local methods based on performance and margin.

Checklist - Quick launch

Enable HTTPS and confirm Shopify payment region settings
Activate Shop Pay, Apple Pay, Google Pay
Add PayPal and one BNPL option if AOV > $150
Test refunds, partial refunds, and subscription cancellations
Reconcile first two payouts and document any discrepancies

Implementation sample command (for engineers)

Use Shopify Admin and Stripe/PayPal dashboards plus webhooks for automated reconciliation:

curl -X POST -H "Stripe-Signature: ..." -d "payload"

By following this guide, you will choose and implement the best shopify payment app for your business needs, reduce friction for customers, and control payment costs as you scale.

Best Shopify Payment App Guide