Supplier invoice audit that checks every line against the contract before you pay it
Overcharges caught against contract, rate card and PO before payment.
See one case, screen by screen ↓Checking each supplier invoice line against the contract, rate card, PO and delivery records to find what was billed above contract. Supplier Invoice Audit does it before payment, on every line of every invoice: agents lay each line beside its evidence with the difference in red, and the payables audit lead decides each finding.
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A drug company pays thousands of supplier invoices a week — CROs, CDMOs, central labs, cold-chain carriers, agencies, software. Accounts payable matches each one to its PO and goods receipt on the total and pays it. On a blanket PO for CRO work there is often headroom, so the total passes. Nobody reads the lines against the master services agreement, the SOW amendment and the signed rate card.
That is where the money goes: a CRA hourly rate $20 above the 2026 rate card, two monitoring visits billed that the visit log shows were cancelled or moved, a site management fee with the volume tier left out, an 8% handling fee on pass-through lab kits the contract says are at cost, business-class fares, a duplicate "-R" invoice, Net 30 asked where the contract gives Net 60. If anyone finds it, it is a recovery audit months after payment — and an agreed claim still has to be matched to its credit note.
Estimated split for one monthly CRO invoice with findings, checked by hand and with the solution.
Specialist agents read every invoice, set each line beside its contract, rate card and PO, and draft the recovery claim; the payables audit lead decides each finding.
Quillon Clinical Research sends invoice MCR-26-0917 for VLT-302 monitoring and site management in September 2026: ten lines, $438,322.00, against PO 4500-8790 and MSA-0417 with SOW-VLT302-03 (Amendment 2). Northwind Bio's payment run is Thursday at 14:00. Here is what happens, screen by screen, in the working solution.
Across the top: every invoice held before the run — Quillon $23,065.60, Summit $15,600.00, Brightwater $6,800.00, Harborline $3,803.78, Kestrel $2,012.60, a Corvane duplicate, and 3 new arrivals to check. The Quillon invoice is open as a ledger: billed $438,322.00, per contract $415,256.40, above contract $23,065.60, with the difference in red on each line and a recovery tracker beside it.
“10 of 10 lines checked against MSA-0417, its rate card and PO 4500-8790 · six agents · 5 above contract”
The invoice reader takes the ten lines, header and payment terms from the e-invoice. The contract terms librarian assembles MSA-0417's terms with their clauses. The three-way matcher pulls PO 4500-8790 and, from the clinical trial system, the visit log — 12 visits completed — and 38 active sites. Then the rate and tier, pass-through and expense, and duplicate and terms checks run on every line. The evidence view puts the invoice, the contract and the evidence side by side, with the source document highlighted.
Each step is on screen with its time — the invoice reader 3.1 s, the contract terms librarian 4.4 s.
486 monitoring hours billed at $180.00. Exhibit B, the 2026 rate card signed on Jan 9, 2026, sets $160.00. $180.00 is the rate in Quillon's unsigned 2027 proposal of Aug 14 — 15.9% above the 2025 rate of $155.34, beyond the 3% cap in §4.3 — and no change order lists it. 486 h × ($180.00 − $160.00) = $9,720.00.
The contract terms librarian's rule: the latest signed amendment wins; drafts are ignored.
Quillon bills 14 on-site monitoring visits. §5.4 bills completed visits only, and the September visit log shows 12: the Site 118 visit on Sep 24 was cancelled and Site 131 moved to Oct 6, so it belongs on the October invoice — $4,900.00. Amendment 2 sets $980 for each active site above 30; all 38 were billed at $1,150 — $1,360.00.
The three-way matcher takes quantities from the delivery records, never from the invoice.
The central lab kits are billed at the receipt amount, $58,420.00, as §7.2 requires — then an 8% handling fee of $4,673.60 is added on top, which §7.2 rules out. Two business-class fares, Boston–Chicago and Newark–Atlanta, are both under three hours; §7.4 allows economy under six hours, and the economy fare on the same flights was $1,006.00 — $2,412.00 above the contract.
“Section 7.2 rules out any handling fee on pass-through costs. The lab kits are already billed at the receipt amount, so the whole 8% line is extra.”
Priya disputes the five findings, each with the amount withheld. The dispute letter writer drafts RC-122 to Quillon's billing team from only the items she disputed, citing Exhibit B, §5.4, §5.2, §7.2 and §7.4. The duplicate and terms sentinel has also flagged the terms row: the invoice asks Net 30, due Oct 31; §9.1 gives 60 days from receipt of a correct invoice, so the undisputed amount is due Dec 6, 2026.
The letter: “We are paying the undisputed $415,256.40 on Dec 6, 2026 under section 9.1 and withholding $23,065.60.”
Approving the short-pay shows what was billed, what is withheld across the 5 disputed items and what is payable on contract terms, with the letter in full. Because the claim is over $10,000, Omar Haddad, category manager for clinical and manufacturing, co-signs after Priya. Nothing is sent until both have approved.
The dispute letter writer never sends — a person approves every supplier letter.
RC-122 goes to billing@quillon-cr.example on Oct 7 and moves to Sent to supplier. The letter asks for a credit note for the withheld amount, or a corrected invoice, within 30 days, with the clause text and evidence for each item attached. The tracker's next steps are Supplier agreed and Credit note received — expected $23,065.60, matched automatically.
“If you see it differently, reply with the document that supports your figure and we will look at it within five business days.”
Corvane Analytical Labs sends CAL-7781-R for stability testing on Corventa lot CR-2214 — $22,750.00. Every line matches invoice CAL-7781, already paid, and the "-R" copy does not reference or cancel the original; TSA-0712 §8.3 says each service is invoiced once. It is blocked, not paid, and claim RC-119 asks for the cancellation.
The sentinel blocks a duplicate before payment, and never cancels a paid invoice.
Harborline Logistics' cold-chain invoice HL-1005-4502 for Oct 1–5 arrives at 09:02, $28,581.11. Priya runs the audit: three lines match TSA-0933, and a residential delivery surcharge of 4 × $310 = $1,240.00 does not — all four deliveries went to hospital pharmacies, which the schedule treats as commercial addresses. Under $10,000, she approves the claim alone.
The same invoices, seen by the five people who answer for them — what their week looked like, and what it looks like now.
Specialist agents read every invoice, set each line beside its contract, rate card and PO, and draft the recovery claim; the payables audit lead decides each finding.
Reads PDF and e-invoices — header, lines, quantities, rates, tax and payment terms — and cites each field.
Finds the supplier's agreement, SOWs, amendments, rate cards and rebate schedules, and keeps a terms sheet with clause citations.
Matches each line to the PO, the goods receipt or service entry, and delivery records such as the visit log and the active-site list.
Checks the arithmetic on every line: contracted rate, escalation cap, volume tiers, discounts and index-linked surcharges.
Checks pass-through costs against receipts, markups and handling fees, travel class and fees the contract does not allow.
Looks back 24 months for duplicates and compares the invoice's payment terms with the contract.
Drafts a courteous dispute or claim letter from the items a person disputed, citing each clause.
Decides each finding, approves the letter. The agents propose; a named person decides.
Ask in plain words, or tell it what to check. It answers from the invoices, the contracts and rate cards, the POs and receipts and the visit logs, and cites the exact line and clause.
Why is the Quillon invoice on hold?
INV-24117 bills $438,322.00. Five lines differ from MSA-0417 by $23,065.60: CRA rate $180 vs $160 ($9,720.00); 14 visits billed, 12 completed ($4,900.00); sites above 30 at $980 ($1,360.00); 8% handling on pass-through ($4,673.60); business-class fares ($2,412.00). It also asks for Net 30; the contract gives Net 60, so the undisputed $415,256.40 is due Dec 6.
Which suppliers leak the most this quarter?
Harborline leaks most often — fuel surcharges above the index band. Quillon leaks the most money (about $593K): rates above the 2026 card and handling fees on pass-through costs. The supplier heatmap is open on the Dashboard.
Add a check: hold CRO invoices that bill more visits than the visit log
Done. New check: Visits billed against the visit log — on every CRO invoice, the billed on-site visits are compared with the visits marked completed in the clinical trial system for the same period. On this week's invoices it matches one: INV-24117, 14 billed against 12 completed, already held. The check is live in Settings and recorded in the audit trail.
Draft the 2025 rebate claim to Quillon
Drafted RC-121 to Quillon Clinical Research for $142,320.00. In 2025 we paid $11,860,000 across three SOWs; §9.5 gives a 1.2% rebate once a year passes $10,000,000, due by March 31. No credit note is in the ERP. Because it is over $100,000, Omar Haddad and Dana Okafor co-sign after you.
13 screens from the working solution, on its sample data. Pick one to see it large.
When invoices are held, who approves and which checks run on every line are settings, and each change goes on the audit trail.
| Setting | Default | Choose from |
|---|---|---|
| Payment run | Thursdays, 14:00 | Thursdays, 14:00 · Tuesdays and Thursdays, 14:00 · Daily, 16:00 |
| Hold an invoice when its findings reach | $250 | $250 · $1,000 · $5,000 — below it, the invoice is paid and the amount claimed back afterwards |
| Rounding tolerance per line | $0.50 | Step up or down; differences this small are treated as a match |
| Release clean invoices automatically | On | On · Off (every invoice waits for a person) |
| Letters up to $10,000 | Priya Raman decides findings and approves the letter | Priya Raman · Lena Ortiz |
| $10,000 to $100,000 | Omar Haddad · clinical & manufacturing co-signs | Omar Haddad · clinical & manufacturing · Lena Ortiz · indirect |
| Over $100,000 | Dana Okafor, finance controller, co-signs as well | Dana Okafor |
| Checks on every line | Rates, rate cards and yearly increases · Volume tiers, discounts and rebates · Billed against delivered · Pass-through costs and expenses · Duplicates · Payment terms | Each on or off · describe a new check in plain words |
Every figure is labelled: a target the solution is built to, an estimate, a typical published result, or a proven one.
“demo” = seen in the working solution, on its sample data · “target” = the design goal, measured in the live solution · “estimated” = our estimate. Context: SOX §404 on payment controls; ICH E6(R3) on sponsor oversight of service providers. People, companies, contracts and invoices named on this page are fictional — characters and sample data in the working solution.
Checking each supplier invoice line against the contract, rate card, PO and delivery records to find what was billed above contract. Supplier Invoice Audit does it before payment, on every line of every invoice: agents lay each line beside its evidence with the difference in red, and the payables audit lead decides each finding.
It reads the CRO's invoice against the master services agreement, the SOW and its amendments and the signed rate card, and matches quantities to the PO, service entries, the visit log and the active-site list from the clinical trial system. Rates above the card or the escalation cap, visits billed but not completed, tiers not applied and markups on pass-through costs are each shown with the clause.
Rates above the signed rate card or yearly cap, volume tiers, discounts and rebates not applied, markups and handling fees on pass-through costs, more billed than delivered, expenses outside policy, fees not in the contract, duplicates across 24 months of paid invoices, and payment terms shorter than the contract's.
No. Its connections are read-only, and a short-pay posts only after a person approves it. Clean invoices release to the payment run, and the undisputed part of a held invoice is paid on the contract's terms.
Yes. The payables audit lead disputes or accepts every finding, and accepting one takes a reason. The dispute letter writer drafts only from disputed items and never sends: a person approves every supplier letter, the category manager co-signs over $10,000 and the finance controller over $100,000.
Yes. A post-payment sweep checks paid invoices from the last 24 months for rebates and tiers that were never credited — in the working solution it found Quillon's 2025 volume rebate, $142,320.00, not credited. Each recovery is tracked from the finding to the credit note.
Yes. The payment run, the hold threshold, the rounding tolerance per line, automatic release of clean invoices, the approvers by amount and each check are settings, and a new check can be described in plain words. Every change goes on the audit trail.
The Agentic Solution Engine builds and deploys it from your requirements and documents — your contracts, rate cards and a sample of past invoices — and it goes live once every quality gate has passed. We will walk you through it on your own invoices first.
Every CRO bid compared like for like, each number traced to its page.
1-min demoContract Obligation ManagementNo missed renewal or rebate, each term linked to its source page.
1-min demoProcurement Intake ManagementEvery request routed the right way, contracts first, and to a PO in under two days.
1-min demoWe'll run Supplier Invoice Audit on a sample of your own supplier invoices and contracts.