Payment provider for an agency that builds online checkouts for many clients

If you’re building checkouts for separate client businesses, start with Stripe and keep each client’s payments in their own Stripe account. That keeps the client as the merchant, rather than routing all their sales through your agency. Stripe also has a partner program for agencies and service providers. (stripe.com)

If you want to earn ongoing revenue from the processing on checkouts you build, Conduit specifically markets an agency integration program: it says it handles merchant onboarding and support while the agency earns a share of processing revenue. Compare its pricing, support, and contract terms with Stripe before choosing. (conduitpaysolutions.com)

Stripe Connect is a better fit if you’re building a platform that centrally onboards many businesses, manages their payments, or routes payouts—not just setting up checkouts for clients. (stripe.com)

Short version: ordinary agency builds → client-owned Stripe accounts; agency wants processing revenue → evaluate Conduit; platform with centralized payment flows → Stripe Connect.

The right provider depends on one question: does your agency ever receive client money, or does each client's money go straight to the client?

If each client gets paid directly (most common for agencies): Stripe is the usual default. One source describes Stripe as best for agencies with developer resources that want customizable online payment experiences. Each client gets its own account, so you build the checkout and the client keeps the funds. Stripe's published rate is 2.9% + $0.30 for US online cards, with no monthly account fee, so there's little overhead per client. Check the partner or agency program terms on Stripe's site, since I didn't verify its current agency benefits.

If your agency collects money and pays out to clients or sellers: This is a marketplace model, and you need a platform product. Stripe Connect is the common starting point, but one comparison notes that Stripe Connect charges a flat rate per transaction regardless of volume, which can hurt at scale. Alternatives include Ryft, Mangopay, Adyen for Platforms, and PayPal Braintree. Be aware that the liability setup matters: on a Stripe destination charge, a chargeback is debited from the platform's balance, and on a direct charge, the same chargeback lands on the seller. Decide this before you build.

Other options:

• Braintree (PayPal): Good if PayPal and Venmo wallets matter to your clients. One source puts it at the cheapest per transaction for most businesses at 2.59% + $0.49, though another lists 2.89% + $0.29, so confirm current pricing.
• Adyen: Better for large, multinational clients. For earlier-stage or lower-volume teams, Adyen's contract and review process add friction, and one source says Adyen pricing is quote-based, implementation requires extensive resources.

My suggestion: Start with Stripe, with each client on their own account. Move to Connect or a platform provider only if your agency needs to hold or split funds. If many of your clients rely on PayPal, add Braintree as a second option.

Fee figures come from third-party blogs, so check the official pricing pages before you commit. If you tell me your rough monthly volume, client countries, and whether you hold funds, I can narrow this down.

For an agency building custom checkout experiences for multiple clients, you need a platform-oriented payment provider that supports "embedded payments" or "marketplace" infrastructure.

Standard payment gateways are designed for a single business owner; what you need is a system that allows you to manage many distinct merchants (sub-merchants) under one umbrella while handling compliance, payouts, and payment splitting on their behalf.

Top Recommendations for Agencies & Platforms

1. Stripe Connect (Best for Flexibility & Developers)

Stripe Connect is the industry standard for agencies and software platforms that need to build customized checkout flows.

• Why it fits: It is designed specifically for multi-party payments. You can onboard your clients as "connected accounts," customize the checkout experience using Stripe Elements, and automate the process of splitting payments (e.g., taking your agency’s fee before passing the remainder to your client).
• Key Advantage: Unmatched developer tools, extensive documentation, and massive global reach. It allows you to maintain full control over the user experience.

2. Adyen (Best for Enterprise & High Volume)

If your agency works with large-scale enterprises or platforms with high transaction volumes across multiple countries, Adyen is the top choice.

• Why it fits: It offers a "unified commerce" approach, meaning you can handle both online and in-person (POS) payments seamlessly.
• Key Advantage: It is an acquirer itself, which often leads to better authorization rates and deeper control over the payment stack for high-volume businesses.

3. Mollie (Best for European Platforms)

If your agency is based in or primarily serves the European market, Mollie is highly recommended for its ease of use and local payment method support.

• Why it fits: It offers excellent platform features for onboarding sellers, managing payouts, and handling compliance, all with a very modern, user-friendly API.
• Key Advantage: Great support for local European payment methods (iDEAL, Bancontact, etc.) out-of-the-box, which can significantly boost conversion rates for your clients.

Key Concepts for Your Agency

To choose the right provider, you must distinguish between the "roles" these companies play in your stack:

Summary Decision Guide

• If you want the best API and developer experience: Go with Stripe Connect.
• If you are building a European-focused platform: Go with Mollie.
• If you have massive, enterprise-scale volume: Go with Adyen.
• If you want to avoid all tax and compliance headaches: Look into an MoR (Merchant of Record) model like Paddle.

Pro-tip: Before committing, define whether you want to "own the merchant" (be the one responsible for their compliance and funds) or simply "facilitate the checkout" (where the merchant has their own direct relationship with the payment provider). Most agencies find that Stripe Connect offers the best middle ground between ease of integration and platform control.

If you’re building checkouts for multiple client businesses, the usual setup is for each client to have its own merchant account—rather than running all clients’ payments through your agency’s account. That keeps each client’s payments, verification, reporting, and payouts separate.

Good options:

• Stripe Connect — a strong default if you’re building a repeatable checkout or software platform. It supports connected accounts for each client, with Stripe handling onboarding and identity verification depending on the account setup. ¹³
• PayPal Complete Payments for Platforms — worth considering if PayPal is important to your clients’ customers. It supports partner-led merchant onboarding and multi-merchant platform payments, but requires PayPal approval for live platform credentials. ⁷¹²
• Adyen for Platforms — aimed more at larger or higher-volume platform businesses; supports merchant onboarding, verification, payment processing, splits, and payouts. ⁸¹⁰

Practical recommendation: If you’re an agency providing checkout implementations—not operating a marketplace or payment platform—have each client create or own their own processor account, then integrate it into that client’s checkout. Consider a platform product like Stripe Connect only if you need to onboard and manage merchants centrally, take a platform fee, or route/split funds.

The right choice depends on your country, client locations, payment methods, and who will be responsible for disputes and compliance.