Three‑Way Matching for Site Payments

Implement three-way matching that speeds site payments and reduces disputes.

Define the matching model and shared data

Three-way matching turns sponsor–site payment reviews from subjective haggling into a reproducible control. The concept is simple: every payable should reconcile three things—the contract term (what you agreed to pay), the operational evidence (what actually happened), and the invoice line (what the site billed). The execution is where programs stumble. Start by designing a shared data model that makes matching obvious and explainable. Map budget lines one-to-one to operational triggers: subject visits and procedures from CTMS/EDC, milestone prerequisites from CTMS and eTMF, and cataloged pass-throughs with accepted proofs (e.g., courier confirmations, imaging reads, translation receipts).

Use stable identifiers—study, site, subject, visit, milestone codes—so records align across systems without manual crosswalks. Make evidence standards explicit. Define what constitutes proof for each line type, the tolerance thresholds (e.g., date windows, allowed variances), and the roles who approve exceptions. For participant-facing items, draw a bright line between reimbursements (repayment of documented out-of-pocket costs, often non-taxable when properly documented) and compensation/stipends (time and burden, often taxable).

Keep IRB/EC materials aligned with actual practice and use authoritative references to guide policy; for instance, see the FDA’s perspective on participant payments at FDA subject payment guidance. For cross-border banking data capture and validation (IBAN, SWIFT/BIC) that reduce rejects, the European Payments Council offers a clear overview at EPC SEPA. Finally, encode foreign exchange (FX) policy so conversions are deterministic. Declare the rate source, booking window, and variance thresholds—then record rate source and timestamp on each conversion. When contracts, evidence, and policy are explicit, matching becomes a fast confirm rather than a debate.

Automate matching, holds, and communication

Automate the mechanics so three-way matching scales across studies and countries. Replace email-driven reviews with event-driven payables: when a visit is completed and verified in EDC/CTMS, generate a payable candidate tied to the governing contract rate and evidence; when a site activation milestone’s prerequisites are met (regulatory greenlight, executed contract, essential-document pack in eTMF), generate the start-up fee candidate with links to artifacts. Pre-validate each candidate: syntactic checks (required fields, banking formats like IBAN/BIC where applicable), semantic checks (does a valid rate exist for this site and effective date?), and conformance checks (apply the declared FX and tax rules).

Auto-approve routine items under thresholds and route exceptions with reason codes and playbooks. Give sites real-time visibility to cut disputes. A portal view should show planned, candidate, under-review, approved, scheduled, and paid states; governing contract references; evidence links; withholding and FX details; and hold reasons with precise fix-lists (e.g., missing receipt, invalid IBAN, out-of-scope line). From the site perspective, basic invoicing discipline helps keep payments on track; see ACRP’s succinct guidance at ACRP guidance. To align on what is commonly invoiceable, the Society for Clinical Research Sites provides a useful quick reference at SCRS invoiceables. Maintain segregation of duties and an immutable audit trail throughout.

Every match decision, approval, override, and payment should log who/what/when/why with links to evidence. This shifts work from detective reconciliation to controlled flow—and it’s defensible during audits.

Monitor KPIs and sustain audit readiness

Measure what matters so matching stays fast and clean as studies evolve. Track end-to-end cycle time from event to payable to disbursement; first-pass match rate; exception aging by reason (timing misalignments, missing documentation, invalid banking data, out-of-scope items); and audit-trail completeness.

Break down KPIs by country and site cohort to spot systemic issues early—e.g., IBAN errors in specific regions or repeated evidence gaps for particular line types. Keep a living evidence narrative. Curate a review-ready binder—SOPs, validation summaries, configuration exports, sample transaction trails—that lets auditors trace a payment from trigger to bank confirmation in minutes. Align oversight with modern GCP quality principles so financial controls reinforce what’s critical to trial integrity; the finalized ICH E6(R3) text provides shared terminology for proportional oversight at ICH E6(R3).

Close the loop with quarterly retrospectives: reconcile planned versus actual payments, analyze root causes for exceptions, and feed updates into rate cards, playbooks, and onboarding UX. Over time, three-way matching becomes an invisible control—accelerating payments, shrinking disputes, and increasing trust on both sides of the sponsor–site relationship.