Start with one invoice and the agreement that applied to its shipments. A 3PL invoice audit asks whether each charge has the right basis, quantity and rate. It does not start by assuming the warehouse made an error.
1. Gather the three inputs
Keep the original invoice export, the signed rate card and amendments, and the shipment or warehouse activity records for the billed period. Include credit notes. Check that amounts use the same currency and the same net or gross basis before comparing them. An order’s sales total is not a warehouse invoice.
2. Confirm what each row represents
A line may represent an order, a parcel, a picked item, a pallet-day or a surcharge event. Match invoice references to the right event. Two parcels for one order can legitimately create two carriage charges. A repeated order reference alone does not prove a duplicate. See the invoice reconciliation guide.
3. Apply the rate valid for the activity
Check the agreed effective dates and any service or quantity conditions. In a hypothetical contract, the first picked unit costs £1.20 and each additional unit £0.35. Three fulfilled units give £1.20 + 2 × £0.35 = £1.90. An invoice charge of £2.25 creates a £0.35 difference to investigate, provided those units and terms are confirmed.
4. Separate differences from missing evidence
A known expected amount supports a comparison. Missing packed weight, dimensions or a shipment match supports a request for evidence, not an overcharge claim. Record the amount billed and what is missing. Prioritise supported positive differences, then high-value lines that remain unresolved.
5. Keep a query record
For each finding, retain the invoice and row, shipment reference, charged amount, expected amount where known, difference and applicable contract rule. Ask the provider to explain or correct the specific line. Check its response against later credits rather than counting a query as a recovery.
Where WarehouseAudit helps
WarehouseAudit performs a deterministic first pass on supported charges. The public trial needs supported invoice and ShipHero dispatch CSVs plus a YAML rate card. Its dimensional and surcharge checks exclude storage, minimum charges and bundle picks. The Shopify app uses fulfilment activity for supported pick and surcharge checks; carriage still needs other evidence. Run a free 3PL invoice audit or check your files with us.
Ready to check your own invoice?
See the 3PL invoice audit workflow for supported inputs, a charge comparison and the route to running your first check.