Last reviewed: 5 June 2025

Quick answer: If you pay US-based affiliates more than $600 by ACH, wire, or check, you must issue a Form 1099-NEC—but PayPal or credit-card payouts are reported instead on Form 1099-K by the processor, so you file nothing. (Source: ReferralCandy Help)

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Disclaimer: The information in this article is provided for general educational purposes only and does not constitute legal, tax, or accounting advice. Tax regulations change frequently, and their application can vary based on your specific circumstances. Always consult a qualified tax professional or legal advisor before acting on any information presented here.

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Table of Contents

1. Why 1099 Compliance Matters
   
   
2. When a 1099-NEC Applies to Affiliates
   
   
3. 1099-K vs 1099-NEC vs 1099-MISC
   
   
4. Collecting W-9s & Tracking Payouts
   
   
5. Automating Tax Forms Inside Your Stack
   
   
6. Launch / Optimise Checklist
   
   
7. FAQ
   
   
8. Takeaways

Why 1099 Compliance Matters

Late or incorrect 1099s trigger IRS penalties of up to $310 per form and sour partner relationships. A clear process protects margin and keeps top affiliates happy.

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When a 1099-NEC Applies to Affiliates

• Threshold: Send a 1099-NEC when total annual payments to a US, non-corporate affiliate exceed $600.

• Payment method: Applies only to cash, checks, ACH, or direct bank wires.
  
  
• Deadline: File with the IRS and furnish to the affiliate by 31 Jan of the following year.
  
  
• Non-US partners: Use Form 1042-S instead of a 1099.
  
  

1099-K vs 1099-NEC vs 1099-MISC

• 1099-K: Issued by PayPal, Stripe, or your credit-card processor for payouts made via their network. For 2024 transactions it fires at $5 000 in gross volume, dropping toward $600 over the next few years. (Source: IRS)‍

• 1099-NEC: Issued by you when you pay affiliates directly (ACH, check) for services/commissions over $600.‍

• 1099-MISC: Legacy form; no longer used for non-employee compensation but still covers rent, prizes, etc. Ignore it for affiliate commissions.
  
  

Rule of thumb: If a third-party settlement organisation moves the money, they file the 1099-K; if you push funds yourself, you file the 1099-NEC.

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Collecting W-9s & Tracking Payouts

• Ask every prospective affiliate to upload a completed Form W-9 during onboarding.

• Store W-9 data in your affiliate portal (ReferralCandy Affiliate Plus does this automatically).

• Tag each payout with method (ACH vs PayPal) and cumulative-year amount so you know when someone crosses $600.

• Use accounting software rules to exclude PayPal/credit-card transactions from 1099-NEC calculations.

Automating Tax Forms Inside Your Stack

• ReferralCandy + PayPal: Pay via PayPal MassPay: PayPal handles 1099-K, no further action.

• QuickBooks + ACH: Auto-generate 1099-NEC PDFs for download and e-file.

• UpPromote / Refersion: Built-in 1099-NEC export if affiliates upload W-9s.

• Zapier fallback: Trigger a record in Google Sheets every time an affiliate payout posts; use this sheet for 1099 prep.

Tip: run a quarterly audit so January filing isn’t a scramble.

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Launch / Optimize Checklist

• Add a mandatory W-9 upload field to your affiliate signup form.

• Tag each payout with payment type.

• Review cumulative ACH payments every quarter.

• Schedule 1099-NEC generation on 2 Jan.

• Verify PayPal/credit-card totals match processor 1099-K reports.

• Link to your referral program template for quick policy wording.

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FAQ

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Takeaways

• File 1099-NEC only when you pay US affiliates $600+ directly.

• PayPal/Stripe payouts = processor handles Form 1099-K, so you don’t.

• Collect W-9s up front and tag each payout type to stay compliant without headaches.
  
  

Need more? Check our referral program template for ready-to-use wording.