Below is a practical, end-to-end guide to set up online payments for an e‑commerce site. It covers planning, choosing providers, technical integration options, security/compliance, operations (fees/settlement/refunds), testing, and a final go‑live checklist.

1. Decide what you need

• Payment types: credit/debit cards, digital wallets (Apple Pay, Google Pay), ACH/eCheck, buy-now-pay-later (BNPL), local methods (if selling internationally).
• One‑time vs recurring/subscriptions.
• Multi-currency support and international sales.
• Risk tolerance (high-risk products need special processors).
• Budget: setup, monthly, per‑transaction fees, chargeback costs.

2. Choose a business model and provider(s)

• Two main options:
  • Payment Service Provider (PSP) / all‑in‑one: Stripe, PayPal, Square, Adyen, Braintree, etc. They handle merchant onboarding, payment gateway, fraud tools and often reduce PCI burden. Good for fast setup.
  • Separate Merchant Account + Payment Gateway: you get a merchant account (bank relationship) and a gateway (e.g., Authorize.Net). This used to be common for large volume sellers and can be cheaper at scale.
• For most new e‑commerce sellers in the U.S., a PSP (Stripe, PayPal, Square/Braintree) is simplest and fastest.

3. Account setup & compliance

• Register the business and create merchant/PSP accounts. Expect identity/KYC checks (owner SSN, EIN, bank account). Bank verification can take 1–7 business days.
• Enable two‑factor auth for accounts.
• Get SSL/TLS cert installed on your site (HTTPS mandatory).

4. Integration options (technical)

• Hosted Checkout (recommended for fastest PCI scope reduction): customer is redirected to provider’s hosted payment page (PayPal Checkout, Stripe Checkout). Simpler, faster, lower PCI scope.
• Client‑side tokenization + server API (recommended balance of control and PCI scope reduction): use provider’s JS SDK to collect card data and return a token/payment method ID; send token to your server to create charge. Keeps raw card data off your server.
• Full API / server‑side handling: you handle card data directly (high PCI burden) — avoid unless necessary.
• Plugins: If using Shopify/WooCommerce/Magento/BigCommerce, use official payment plugins (faster setup).
• Mobile SDKs: use iOS/Android SDKs if you have native apps.

5. Basic technical implementation steps (typical with a PSP)

• Create merchant account and get API keys (test and live).
• Add HTTPS and CORS configuration.
• Implement client SDK or hosted checkout to collect payment details and create a payment token.
• Server: use provider API to create a Payment Intent / Charge using token; save order and transaction IDs in your DB.
• Implement webhooks for asynchronous events: payment succeeded/failed, chargebacks, refunds, payout updates. Secure webhooks with signature verification.
• Log all payment activity and store minimal required transaction metadata.

6. Security & PCI compliance

• Use hosted pages or client tokenization to reduce PCI scope (SAQ A or A‑EP vs full SAQ D).
• Never log/store full card numbers or CVV. Store only last 4 digits and tokenized IDs.
• Use TLS 1.2+, strong cipher suites.
• Implement fraud detection: provider’s tools (Radar for Stripe), 3DS2 for SCA (for EU), velocity checks, IP/country checks.
• Maintain secure server practices: regular patching, least privilege, DB encryption at rest for sensitive fields.

7. Fees, settlement, and reconciliation

• Per-transaction fees: typically a percentage + fixed cent amount (e.g., 2.9% + $0.30 in the US) for cards; ACH is cheaper but slower. PSPs have published fee tables.
• Settlement timing: payouts to your bank typically 1–7 days depending on provider, account history, and country.
• Reconciliation: match orders in your e‑commerce system to payouts and fees using provider reports or APIs.

8. Refunds and chargebacks

• Implement a clear refund policy and easy refund flow in your admin panel.
• Respond promptly to chargebacks with evidence (receipts, shipping/tracking, IP logs). Chargeback fees may apply.
• Use fraud tools to reduce chargebacks.

9. Taxes, legal, and accounting

• Collect sales tax where required. Use tax automation tools (TaxJar, Avalara) or platform tax features. Sales tax rules depend on nexus and product type.
• Keep records of transactions for accounting and reconciliation. Integrate payments with your accounting software (QuickBooks, Xero).

10. Testing and launch

• Use provider sandboxes/test modes and test card numbers. Test common flows: success, failed card, expired, 3DS challenge, refunds, partial refunds, webhook delivery/retry.
• Test across devices and browsers. Test UX for failed payments and retry flows.
• Soft launch: start with cap on daily volume or manual review for first few days to catch issues.

11. Monitoring and ongoing operations

• Monitor dispute rates, success rates, API errors, webhook failures, payout delays.
• Keep KYC documents up to date (providers may request updates).
• Periodically review pricing, fraud rules, and payment methods offered.

12. Typical timeline

• Basic setup with hosted checkout or plugin: a few hours to 2 days (plus bank verification).
• Custom integration with tokenization and webhooks: 2–7 days development + testing.
• Full enterprise integration with reconciliation systems and multiple payment methods: several weeks.

13. Quick provider & platform notes (common choices)

• Stripe: developer‑friendly, supports cards, wallets, subscriptions, ACH, international payments, strong webhooks and SDKs.
• PayPal/Braintree: widespread consumer familiarity, PayPal express/checkout options, Braintree for developer integrations.
• Square: easy for omnichannel (in‑person + online).
• Adyen, Worldpay, Authorize.Net: common at larger merchants.
• Shopify/WooCommerce/BigCommerce: use built‑in/official payment plugins for fastest setup.

14. Minimal recommended setup for a small e‑commerce store (fastest, secure)

• Use a PSP (Stripe or PayPal) with hosted checkout or official plugin for your platform.
• Enable HTTPS, use tokenization, enable fraud prevention tools, set up webhooks, configure refund policy and automated receipts.
• Test in sandbox, verify bank payouts, then go live.

15. Final checklist (before going live)

• Business and bank account linked and verified.
• HTTPS enabled on site.
• Merchant/PSP account in live mode; API keys rotated into production.
• Checkout flow tested (successful and failed cases).
• Webhooks implemented and verified.
• Refund and dispute procedures documented.
• Tax collection settings in place.
• Monitoring/logging for payments enabled.

If you want, tell me which platform/stack you’re using (Shopify, WooCommerce, a custom site with Node/PHP/Rails, etc.) and I’ll provide a concise, tailored step‑by‑step integration checklist and sample code for that environment.