WooCommerce affiliate programmes were typically powered by AffiliateWP, YITH WooCommerce Affiliates, or custom integrations. These plugins store affiliate relationships, tracking codes, commissions, and payment history in WordPress database tables that are entirely separate from Shopify's data model. Migration to Shopify requires selecting a new affiliate management app and manually recreating affiliate relationships — the historical commission data cannot be directly migrated. This guide covers selecting the right Shopify affiliate app, migrating affiliate relationships, and setting up an effective commission structure.

Shopify affiliate app comparison

App	Pricing	Best for
UpPromote	Free tier; from $29.99/mo	Best value for small-medium programmes. Clean affiliate dashboard, good Shopify integration, supports auto-commission via discount codes.
Refersion	From $99/mo	Enterprise-grade tracking, deep analytics, large affiliate network access. Best for established programmes with 50+ affiliates.
GoAffPro	Free tier; from $24/mo	Good free tier, reliable tracking. Good for starting out or small programmes.
LeadDyno	From $49/mo	Email marketing integration, social sharing tools. Good for content creator programmes.
Affiliatly	From $16/mo	Simple, affordable. Good for straightforward percentage commission programmes.

Affiliate tracking methods

Unique tracking link: Each affiliate receives a unique URL with a tracking parameter (e.g., https://yourstore.com?ref=affiliatecode). Clicks and resulting purchases are attributed to the affiliate. Most reliable tracking method.
Discount code tracking: Each affiliate has a unique discount code (e.g., "JANE15"). Purchases using that code are attributed to the affiliate. The code may or may not give a discount (typically 10–15% off for the customer). Simpler for affiliates to share — especially influencers who mention codes verbally in videos.
Combination tracking: Use both — tracking link for web traffic attribution, discount code for offline or social proof attribution. Combined tracking gives the most complete attribution picture.

Commission structures

Percentage of sale: Most common. 10–20% of order value (excluding shipping and VAT). Scales with order value — rewards affiliates who drive high-value orders.
Flat rate per sale: Fixed amount per order (e.g., £5 per order regardless of value). Predictable cost; less incentive for affiliates to drive high-value orders.
Product-specific commission: Higher commission on high-margin products, lower on low-margin. Requires commission rules per product or collection. Refersion and UpPromote support this.
Tiered commission: Commission rate increases with affiliate performance. Example: 10% for 1–10 sales/month, 15% for 11–25 sales/month, 20% for 25+ sales/month. Incentivises higher-performing affiliates.
One-time vs recurring: For subscription products, affiliates can earn on the initial sale only, or on each recurring charge. Recurring commission (15–30% of each payment) is standard for SaaS; for physical products, one-time commission per order is more common.
Cookie window: how long after an affiliate click a purchase is attributed to them. 30 days is standard; 60–90 days for longer consideration cycles.

Influencer and creator programme

Influencer programmes differ from traditional affiliate programmes in scale and relationship type:
- Micro-influencers (1K–50K followers): often paid in product (free product in exchange for a post), may also receive affiliate commission.
- Mid-tier (50K–500K followers): combination of flat fee per post + affiliate commission. Affiliate commission aligns incentives — influencer earns from driving actual sales, not just impressions.
- Large influencers (500K+): flat fee per post. Affiliate commission may also apply but is not the primary incentive.
Dedicated discount codes: give influencers unique codes (typically their name or handle: EMMA20, KAYLAFIT). These double as affiliate tracking and social proof — audiences trust codes from specific creators they follow.
Product gifting tracking: some apps (UpPromote, Refersion) allow "seeded product" gifting orders that do not charge the affiliate but are recorded as a relationship with them.
Content brief: provide influencers with a brief specifying what to show, key messages, and required disclosures (UK ASA requirements: #ad, #gifted on paid/gifted content).

Migrating existing affiliate relationships

Export affiliate data from WooCommerce (AffiliateWP or YITH): affiliate name, email, current commission rate, payment method, total earnings to date.
Communicate migration to affiliates: inform all active affiliates that the programme is moving to a new platform. Provide their new tracking link or discount code in the migration communication email.
Historical commission balances: if affiliates have unpaid commission from WooCommerce, pay these out via the old system before migration (or manually via bank transfer) before the new system goes live.
Recreate affiliate accounts: manually create affiliate accounts in the new Shopify app for all active affiliates. Import their email, commission rate, and unique code/link.
Programme terms: if your affiliate programme had specific terms (payment thresholds, prohibited promotional methods), confirm these carry over in the new programme documentation.

Payment management

Payment threshold: minimum balance before payout. Standard: £50 or £100 minimum. Prevents many small micro-transactions.
Payment schedule: monthly payment is standard. Some programmes pay on Net 30 (30 days after sale to allow for returns).
Payment methods: PayPal is the most common affiliate payment method. Some apps (Refersion) support Stripe and bank transfer.
Returns handling: when an order is returned, the commission should be reversed. Most apps handle this automatically if the order is refunded in Shopify. Verify your app's refund handling before going live.
UK tax: affiliates earning above the £1,000 trading income allowance must declare earnings to HMRC. This is the affiliate's responsibility, not the retailer's. However, for affiliates earning above a threshold, a 1099-equivalent self-billing arrangement may be appropriate.

Affiliate migration checklist

Choose Shopify affiliate app: UpPromote (recommended), Refersion (large programmes), GoAffPro (budget)
Export affiliate data from WooCommerce: emails, commission rates, unpaid balances
Pay outstanding commissions via old system before go-live
Communicate migration to all active affiliates with new tracking link/code instructions
Recreate affiliate accounts in new Shopify app
Configure commission structure: percentage, rate, cookie window
Configure payment settings: threshold, schedule, method
Test affiliate tracking: click affiliate link → purchase → commission appears in affiliate dashboard
Test discount code tracking: use affiliate code → purchase → attributed to correct affiliate
Test return handling: refund an order → commission reversed

The affiliate communication at migration is the moment of highest relationship risk. Affiliates are essentially business partners — they have invested effort into promoting your store, and if their tracking links break, their commission history disappears, or their payment setup changes without warning, they will feel disrespected and will stop promoting. A well-managed affiliate migration communication — specific, clear, early, and appreciative — takes 2 hours to write and prevents months of affiliate relationship damage. Include: what is changing, when it is changing, what they need to do (set up new account, use new link), when any outstanding commissions will be paid, and a personal thank you from the founder or affiliate manager. The stores that handle this correctly often find that migration communication improves affiliate engagement because it demonstrates that the brand values the relationship enough to communicate proactively.

Shopify affiliate programme setup after WooCommerce (2026)