I need to pick a payment API for a SaaS startup that charges monthly subscriptions and also takes one-time setup fees. Recommend the main options and what to watch out for.

For a SaaS startup with monthly subscriptions + one-time setup fees, you’re usually choosing between a billing-first platform and a payments-first platform.

Short recommendation

• Best default for SaaS billing: Stripe Billing
• Best if you want enterprise billing, invoicing, and complex revenue ops: Chargebee or Recurly
• Best if you want simple checkout and direct processor: Stripe only
• Best if you’re selling globally and want more local payment methods built in: Paddle or Adyen (depending on your needs)

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Main options

1) Stripe Billing

Best for: Most SaaS startups

Why people pick it

• Excellent API and developer experience
• Supports:
  • recurring subscriptions
  • one-time setup fees
  • trials
  • coupons/promo codes
  • proration
  • usage-based billing
• Strong ecosystem: tax, invoicing, checkout, customer portal, webhooks
• Easy to start small and scale

Watch out for

• Billing logic can get complicated quickly if you need lots of plan variations
• You may need to build some subscription management workflows yourself
• Tax/compliance features may require extra Stripe products or third-party tools
• Refunds, disputes, and failed-payment retry logic need careful handling

Good fit if

• You have a product team that can implement billing flows
• You want speed and flexibility
• You expect to grow into more complex billing later

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2) Chargebee

Best for: SaaS companies that want billing ops features on top of a payment gateway

Why people pick it

• Strong subscription management
• Good for recurring billing, invoicing, dunning, trials, coupons, metered billing
• Can sit on top of Stripe, Adyen, Braintree, etc.
• Better out-of-the-box billing workflows than a raw payments API
• Helpful if finance/ops teams need more control

Watch out for

• More expensive than using Stripe alone
• Extra system layer means more complexity
• Integration and maintenance can be heavier than a direct payment processor
• You still need to manage the underlying gateway relationship

Good fit if

• You have more complex billing operations
• You want less custom code for invoicing/retries/collections
• You need flexibility across multiple processors

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3) Recurly

Best for: Subscription-heavy businesses that want mature billing tools

Why people pick it

• Built for recurring billing
• Strong dunning and subscription lifecycle management
• Solid support for coupons, upgrades/downgrades, proration, retention flows
• Good for businesses with more established billing needs

Watch out for

• Can be less appealing for very early-stage startups due to cost/complexity
• API/developer experience is often viewed as less modern than Stripe
• Still an additional platform to operate

Good fit if

• Billing is central to your business
• You want robust subscription operations from day one

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4) Paddle

Best for: SaaS with global customers and desire for simpler tax/compliance handling

Why people pick it

• Often acts as merchant of record
• Handles a lot of tax/VAT/sales tax complexity
• Useful if you want less compliance burden
• Can simplify international selling

Watch out for

• Less control than Stripe-style direct processing
• Pricing/model may be less flexible depending on your business
• Not ideal if you want to deeply customize payment flows
• Merchant-of-record model may affect reporting/branding/customer experience

Good fit if

• You want to minimize tax and compliance headaches
• You sell globally and want a faster path to international billing

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5) Adyen

Best for: Larger or more global companies, or those needing many payment methods

Why people pick it

• Very strong global payment coverage
• Good for enterprise-scale payment operations
• Supports many local payment methods and currencies
• Excellent for multi-channel or higher-volume use cases

Watch out for

• More enterprise-oriented; can be overkill for an early startup
• Integration and setup may be heavier
• Billing/subscription workflow may need more custom work or an added billing layer

Good fit if

• You expect international scale quickly
• You need broad payment method support

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What to watch out for

1) Subscriptions + one-time fees

Make sure the platform can handle:

• recurring subscription charges
• one-time setup fees on signup
• optional add-ons
• upgrades/downgrades with proration
• free trials and deferred billing

Some systems handle these cleanly; others require custom invoice logic.

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2) Failed payments and retries

You’ll want:

• automatic retries
• card updater support
• dunning emails
• grace periods
• suspension/reactivation rules

This is a common source of churn if not handled well.

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3) Taxes and compliance

Ask:

• Does the platform calculate sales tax/VAT?
• Does it support invoicing tax details?
• Who is responsible for remittance?
• Do you need tax registration in multiple regions?

If you sell internationally, tax handling can become a major operational burden.

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4) Invoicing and accounting

Check whether you need:

• invoices for all charges or only some
• credit notes/refunds
• revenue recognition support
• exports to accounting tools like QuickBooks, Xero, NetSuite, etc.

Finance teams often care about this more than product teams do.

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5) Customer self-service

Useful features include:

• update card details
• download invoices
• cancel plan
• change plan
• see billing history

A customer portal reduces support load.

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6) Webhooks and operational reliability

Billing systems live and die by event handling:

• payment succeeded/failed
• subscription created/updated/canceled
• invoice paid/open/voided
• charge disputed/refunded

Make sure your backend is built to handle webhooks idempotently and reliably.

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7) Pricing structure

Compare:

• transaction fees
• subscription/billing platform fees
• dispute fees
• international card fees
• currency conversion fees
• tax product costs
• invoicing/email costs

A “cheap” provider can get expensive depending on your mix of customers.

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8) Checkout conversion

Look for:

• support for saved payment methods
• Apple Pay / Google Pay
• local payment methods
• one-click checkout
• mobile-friendly checkout

Even small improvements here can materially raise conversion.

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Practical recommendation by stage

If you’re early-stage and want speed:

Stripe Billing

• Fastest path
• Best developer experience
• Enough for most SaaS subscription models

If you expect billing complexity and finance ops needs:

Chargebee + Stripe/Adyen

• Better billing operations
• More scalable for complex monetization

If you want global tax simplicity:

Paddle

• Good for reducing compliance burden

If you’re enterprise/global from the start:

Adyen

• Strong payment infrastructure, but heavier lift

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My default pick

For most SaaS startups, I’d recommend:

Stripe Billing + Stripe Checkout/Customer Portal + Stripe Tax if needed

That gives you:

• subscriptions
• one-time setup fees
• trials/coupons/proration
• good UX
• strong APIs
• room to grow

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If you want, I can also give you a side-by-side comparison table of Stripe vs Chargebee vs Paddle vs Recurly based on your specific startup stage, geography, and pricing model.