Below is a practical, end-to-end guide to set up online payment systems for an e-commerce store — from choosing a model to launch, security, and ongoing operations.

1. Decide what payment model you want

• All-in-one (payment service providers): Stripe, PayPal, Square, Adyen, Shopify Payments, etc. Pros: fast setup, no separate merchant account, good SDKs. Cons: slightly higher fees, fewer bespoke features for very large merchants.
• Gateway + merchant account (payment gateway + separate acquirer): For high-volume or specialized needs. Pros: lower per-transaction costs at scale, flexibility. Cons: more setup complexity and contracts.
• Marketplaces / platforms: Use platform-managed payments if selling on a marketplace (they handle payments/funding).
• Alternative (pay-later, wallets, bank transfers): Add BNPL (Affirm/Klarna), digital wallets (Apple Pay, Google Pay), and ACH/e‑check for lower fee alternatives.

2. Choose the payment methods to accept

• Credit/debit cards (Visa, Mastercard, Amex, Discover)
• Digital wallets (Apple Pay, Google Pay, PayPal, Venmo for commerce)
• ACH / bank debits (for US recurring or high-value)
• Local/country-specific methods (Alipay, WeChat Pay, SEPA, iDEAL, etc.)
• Buy Now Pay Later (Klarna, Affirm)
• Gift cards and store credit

3. Pick a provider(s)

• For most small-to-medium e-commerce stores, Stripe or PayPal are the fastest/most flexible options. They provide API, hosted checkout, SDKs, webhooks, fraud tools, and payouts.
• If on Shopify/BigCommerce/WooCommerce there are built-in integrations (Shopify Payments, WooCommerce + Stripe, etc.).
• Consider pricing (transaction fee % + flat fee), payout frequency, supported countries/currencies, chargeback policies, developer docs, and compliance support.

4. Set up business and merchant requirements

• Business bank account and legal entity information (for payouts and KYC).
• Tax registration and sales-tax/VAT setup for the regions you sell into.
• Prepare documentation for provider KYC (EIN/SSN, address, bank details, business registration).

5. Integration approaches (choose one)

• Hosted checkout (redirect or overlay): Easy and PCI-light — customer enters card details on provider pages (e.g., PayPal Checkout, Stripe Checkout). Good for quick, secure integration.
• API / custom checkout with tokenization: Keep full brand control. Use the provider’s client-side tokenization (Stripe Elements, PayPal JS SDK) so your server never handles raw card numbers. This is flexible but requires more dev work and security controls.
• SDKs & mobile: Use mobile SDKs for in-app payments and native wallet support.
• Headless / server-side: For complex flows (multi-step checkout, subscriptions), combine client tokenization + server API calls + webhooks.

6. Security & compliance

• PCI DSS: If you use hosted checkout or tokenization correctly, your PCI scope is minimized. If you handle raw card data, you must achieve full PCI compliance (avoid unless necessary).
• TLS/SSL: Always serve checkout pages over HTTPS with a valid certificate.
• Use tokenization: Never store card numbers unencrypted; rely on tokens from your payment provider.
• Webhooks: Secure webhooks (signatures, replay protection) for payment status notifications.
• Data retention: Only store what you need; encrypt sensitive data at rest.
• SCA (Strong Customer Authentication): For EU customers, support 3D Secure / SCA workflows (most gateways handle this).
• Fraud prevention: Use provider tools (Radar, Risk API) and 3rd-party solutions. Set velocity/amount rules and require CVV/AVS where appropriate.

7. Implement business flows

• One-time purchases
• Recurring/subscriptions (billing schedules, proration, trials)
• Refunds and partial refunds
• Chargeback handling process (evidence collection, timeline)
• Failed-payment retries and dunning for subscriptions

8. Development & testing checklist

• Use sandbox/test mode accounts and test card numbers (do not test with real cards).
• Test all payment outcomes: success, failure, declined, 3DS required, partial captures, refunds, cancellations.
• Test webhooks: validate signature and idempotency (handle duplicate events).
• Test edge cases: interrupted checkout, currency mismatches, network failures.
• Logging and monitoring for payments & errors.

9. UX & conversion best practices

• Keep checkout simple and mobile-friendly.
• Offer guest checkout and saved cards (with explicit consent).
• Show trusted badges, transparent pricing, and full charges + shipping before final confirmation.
• Pre-fill known info; use autofill-friendly fields.
• Offer multiple payment options but don’t overwhelm — pick 2–4 primary methods for your audience.
• Provide clear success/receipt pages and order confirmation emails.

10. Pricing, fees, and reconciliation

• Understand per-transaction fees, currency conversion fees, chargeback fees, monthly fees, and payout costs.
• Set up monthly reconciliation: map platform payouts to orders (providers give payout reports).
• Use accounting integration or export CSVs to your accounting software.

11. Legal, taxes, and policies

• Update Terms of Service, Privacy Policy, Refund Policy, and Cookie Policy.
• Display return/refund policies prominently before purchase.
• Ensure sales-tax/VAT collection; use tax engines (TaxJar, Avalara) if needed.

12. Launch & operations

• Soft-launch to a subset of users or internal customers.
• Monitor payments, latency, failed payments, chargebacks for first 30–90 days.
• Train customer support on payment states, refunds, and dispute handling.
• Schedule periodic security reviews and re-evaluate fees & providers annually.

13. Ongoing improvements

• Analyze payments funnel for drop-off and optimize.
• Add local payment methods as you expand internationally.
• Revisit fraud rules, KYC thresholds, and refund/chargeback policies.
• Consider adding installment/BNPL or subscription-management features if business model needs them.

Quick sample implementation path (small business, minimal dev):

1. Create Stripe (or PayPal) account, complete KYC.
2. Enable Stripe Checkout + Apple/Google Pay in dashboard.
3. Add Checkout link or use provider plugin for your platform (WooCommerce/Shopify).
4. Configure webhooks for payment succeeded / failed.
5. Test in sandbox with sample cards, then enable live keys.
6. Launch and monitor.

Estimated time & cost

• Time: Hosted checkout + plugin: a few hours to a few days. Custom API integration: 1–4 weeks depending on complexity. Larger/multi-country rollouts: months.
• Cost: Setup costs are usually minimal. Expect transaction fees ~1.9–3.5% + $0.20–$0.50 per transaction depending on provider and card type; possible monthly fees for gateways or higher-volume discounts.

If you want, I can:

• Recommend specific providers based on your platform, country, monthly volume, and target payment methods.
• Provide example code snippets for Stripe Checkout, Stripe Elements, or PayPal integration.
• Give a one-page checklist tailored to Shopify, WooCommerce, or a custom site.

Which platform or provider are you using (Shopify, WooCommerce, custom site, other)? I can give concrete steps or code next.