Quick answer: Most ecommerce brands pay affiliates through PayPal, bank transfer, or Wise, and use a clear affiliate payment schedule with automated tracking so partners are paid on time in multiple currencies. Modern Shopify-ready apps trigger payouts from order data and support cash or store-credit rewards.
Payouts are the moment of truth for your program. If partners get paid reliably, they post more, send more clicks, and stay loyal. The payout method you choose affects fees, speed, and whether overseas creators can participate easily. For DTC brands, a platform that automates tracking and payouts removes manual work and gives a single source of truth for commissions.
You can also grow performance faster by pairing affiliates with referrals in one stack. That way, customer-led revenue and creator-led revenue roll up in the same dashboard and process.
On Shopify and similar carts, an affiliate app creates links or codes, records orders, and then triggers payouts based on your rules. Payout types can be cash, flat fees, revenue share, or store credit. The better tools support multi-currency payments and tag orders automatically so returns or partial shipments do not break your numbers.
If you need a refresher on setup and recruiting, see this [step-by-step guide to launching an affiliate program] which covers installation, rules, and onboarding creators.
Pros: Ubiquitous acceptance, fast settlement, simple for creators. Many apps connect directly to PayPal so you can process batches in a few clicks. Auto-conversion helps when paying in different currencies.
Cons: Fees add up on large payouts or high volumes. Some regions have limited withdrawal options or higher fees. For very high-value partners, direct bank transfer can be cheaper.
Best for: Early to mid-stage programs, global creator mixes, and teams that want quick wins without finance overhead.
Tip: If your audience is social-first, PayPal’s instant payouts can keep influencers engaged between larger monthly runs.
Pros: Low fees at scale, familiar for finance teams, clean audit trail. Great for paying top partners on fixed net-terms or for larger quarterly commissions.
Cons: Cross-border wires can be slow or expensive. Collecting correct banking details takes care. For new or long-tail affiliates, the ops lift is higher than PayPal.
Best for: Enterprise partners, agencies, and high-volume affiliates who prefer net-30 or net-45 settlement with amounts above your PayPal comfort level.
Pros: Multi-currency accounts and favorable FX rates make Wise attractive for international affiliate payouts. Creators can receive in local currency without heavy fees, and you reduce failed payments due to mismatched currencies.
Cons: Some partners may not already use Wise, so you will need to onboard them.
Best for: Programs with a large share of partners outside your home market, or where you pay in EUR, GBP, AUD, or SGD as often as USD. If your app supports multi-currency cash payouts, you already have part of this solved.
Cash is not the only reward. Many ecommerce brands pay part or all of the commission in store credit or gift cards. This reduces cash outlay and drives repeat orders, while still giving a valuable reward. Leading Shopify apps support cash, coupon, or custom rewards, so you can run hybrids like cash for new-customer orders and store credit for repeat-order campaigns.
If you prefer to focus on referral-style perks for customers while keeping cash for affiliates, you can run both in a single dashboard and segment rewards by partner type.
Your affiliate payment schedule is the heartbeat of the program. Pick one cadence and stick to it.
Set a minimum threshold to avoid micro-payments and FX friction. For example, pay out when a partner’s balance reaches $50. List all of this in your public terms and your partner portal so there are no surprises. Track commission payouts alongside EPC, AOV, and revenue by affiliate in your analytics so finance and growth stay aligned.
For US programs, collect W-9s and issue 1099s where applicable. In other regions, collect local equivalents. Several platforms help automate this paperwork during onboarding, so you are not chasing forms at year end.
Fraud controls matter before money goes out. Look for device fingerprinting, IP checks, leaked-code detection, and “new-customer only” rules. These reduce self-referrals, coupon abuse, and low-quality traffic that would otherwise inflate payouts.
If you want payouts without spreadsheet pain, run affiliates and referrals together in ReferralCandy. You get:
Getting started is straightforward. Install the app, define commission rules, create trackable assets, and send your onboarding email. A clear launch plan helps you go live in under an hour. This Shopify guide walks through each step.
For a broader look at Shopify options, here is a round-up of the best Shopify referral apps to compare features and integrations.
Hey, I'm Elmeri Palokangas. I'm an e-commerce and online marketing specialist with over five years of experience. My expertise extends to various publications and companies, including WordStream, QuickMail, Scribe, Marketcircle, and Digital.com. When I'm not enjoying a cup of coffee and writing awesome articles, you can find me running in the nearby mountains.
Grow your sales at a ridiculously
lower CAC.
