3PL invoice reconciliation connects three different records: what was billed, what the contract permits and what actually happened. Matching the total alone is not enough. The records must refer to the same activity and commercial terms.
Invoice: what was charged?
Keep invoice number, row, order or tracking reference, charge type, quantity and net amount. Separate warehouse charges from customer sales totals. A Shopify orders CSV can describe purchases and fulfilment activity, but its Total or Shipping fields do not prove what the 3PL billed your business.
Rate card: what should apply?
Identify the billable unit, rate, effective dates, carrier service and any conditions. Some rules require additional evidence, such as bundle contents or a complete storage period. Use an amendment only where it applies; the latest uploaded contract is not necessarily the correct one for an older shipment.
Activity: what actually happened?
Use successful fulfilments and shipped quantities for outbound work, and separately linked records for returns or receiving. One order can create multiple fulfilments or parcels. Do not force all invoice rows onto the first order match if tracking or other references conflict.
For example, an order for three units ships as two units in one parcel and one in another. Two carriage lines may be legitimate. Whether one or two first-pick fees apply depends on the agreement and how the warehouse records each event. The order count alone cannot settle the comparison.
Keep three outcomes separate
- Looks correct: the supported charge matches the agreed rate and available activity evidence.
- Billing discrepancy: the evidence supports a comparison but the billed amount or quantity differs.
- Needs evidence: the shipment match, applicable rate or operational records are insufficient to complete the check.
If some charges cannot be priced, do not subtract a partial expected total from the entire invoice and call the result an overcharge. Track those charges as unresolved exposure. Check the common billing errors once the references and commercial basis are clear.
Reconcile one invoice first
Choose a period covering the relevant fulfilments and confirm currency and net amounts. WarehouseAudit’s Shopify app uses imported fulfilments for supported checks. The public trial uses supported dispatch files instead and has different check coverage. Neither should invent missing shipment measurements. Run a free 3PL invoice audit or follow the full audit checklist.
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.