Inside Nexa: how Shipsy auto-matches freight invoices and resolves disputes

Shipsy’s Nexa agent reconciles inbound freight invoices against the underlying bookings, rate cards, and execution events — line by line, automatically. Where it finds a clean match, the invoice is approved for payment without human touch. Where it finds a mismatch, Vera, Shipsy’s dispute resolution agent, picks it up with the full audit trail and negotiates with the carrier. The combined loop has reconciled tens of millions of dollars in carrier disputes at a global alco-bev leader operating across 70+ countries.

Why we built this

Freight invoice reconciliation is the single most undermanaged cost center in most logistics P&Ls. Shippers running hundreds of carriers receive thousands of invoices monthly, each with line-item variability (fuel surcharge formulas, detention fees, accessorials, rate-card revisions). Most teams do sample-based checking — meaning 95%+ of invoice lines are paid without verification. A 1-2% over-billing rate at enterprise scale is millions of dollars quietly leaking out.

Shipsy’s reconciliation loop closes the leak by matching 100% of invoice lines to the source-of-truth booking event.

How it works

Rate card ingestion. Every carrier contract is digitized into structured rate cards inside Shipsy — origin, destination, weight break, mode, surcharge formulas, accessorial schedules, effective dates. Rate card digitization is a one-time effort supported by Shipsy’s ingestion tools; once in, it’s the reference for every future invoice match. See rate card digitization + audit.

Expected-cost calculation. At booking time, Shipsy calculates the expected invoice amount for the shipment — base rate + applicable surcharges + expected accessorials. This expected cost is attached to the booking record and travels with the shipment through execution. When the invoice arrives, there’s a baseline to match against.

Invoice ingestion. Carrier invoices arrive via EDI, API, email-PDF, or portal scrape. Nexa parses them into structured line items — each line has shipment reference, charge type, quantity, rate, and total. PDFs go through a specialized parser tuned for major global carrier invoice formats.

Three-way match. For each invoice line, Nexa compares three records: 1. Booking record — the contracted expectation (lane, weight break, service level). 2. Execution record — what actually happened (actual weight captured at hub, actual mileage, actual detention time from driver telemetry, ePOD timestamps). 3. Invoice line — what the carrier is billing.

A line matches when booking × execution × invoice all align to the rate card. When they diverge, Nexa classifies the variance: base-rate error, weight-break error, surcharge error, accessorial overcharge, duplicate bill, or ghost bill (a charge for a shipment that never executed).

Auto-approve or auto-dispute. Matched lines flow to AP for payment without human touch. Unmatched lines are classified by variance type and auto-routed: - Small variances within a tolerance (configurable, typically 1-2%) are logged and paid. - Larger variances are packaged into a structured dispute with evidence (the booking, the rate card clause, the execution event) and handed to Vera.

Vera handles the dispute. Vera constructs a formal dispute message — citing rate card section, shipment ID, and the evidence — and either emails the carrier (for email-based carriers) or files through the carrier’s dispute portal API. Vera tracks the dispute through resolution. Most carriers return a corrected invoice within 5-15 days once presented with a structured, evidence-backed dispute. This is the mechanism that autonomously resolved $25M+ in carrier/vendor disputes at a global alco-bev leader operating across 70+ countries — see the detailed case study.

Exception routing. Disputes that Vera can’t close (genuine contract ambiguity, edge cases) escalate to a named human with the full chain attached. The human makes the judgment call; the decision feeds back into Vera’s playbook for similar future disputes.

Merchant-side reconciliation. For shippers who re-bill customers (3PLs, freight forwarders), Nexa also handles outbound billing accuracy — generating customer invoices from the same execution data, tracking customer payments, and flagging customer disputes to Vera. One loop, both directions.

Early results

Shippers running Nexa at full coverage typically see: 85-95% of invoice lines auto-reconciled within 24 hours of receipt (vs. 10-30% manual sampling pre-Shipsy), 1-3% recovery on total freight spend from variance catches that would otherwise be paid silently, and AP cycle times compressed from 30+ days to under 10. A leading Western European parcel operator with 50%+ national market share uses the loop to reconcile subcontractor invoices at scale across a large regional subcontracted last-mile footprint.

What’s next

Nexa’s next release extends to accessorial prediction — detecting likely accessorial charges at booking time so shippers have a true total-cost-of-shipment view before they commit, not after the invoice arrives. See Nexa’s full settlement automation workflow.