The customer pays one invoice but disputes the other invoice in the same account

One payment does not explain every invoice
A hypothetical contractor has two invoices outstanding for different jobs. The customer pays the first and says the second contains disputed variation work. The contractor treats the receipt as proof that the entire account is accepted. Before making that assertion, match the payment to the customer's instructions and separate the actual dispute from the amount already paid.
Reconcile the allocation evidence
Check the bank reference, remittance and relevant correspondence against the ledger. If the customer identified a particular invoice, preserve that information. If the allocation is unclear or contested, obtain appropriate accounting or legal guidance rather than assigning the money to the oldest invoice solely to strengthen a preferred argument. The record should show the evidence behind the allocation.
Return to the agreed terms and disputed work
Business.gov.au recommends checking payment conditions and discussing unpaid amounts with the customer. For the disputed invoice, gather the contract, variation records and supporting delivery information. Ask which item is challenged and why. A payment relating to another job does not remove the need to understand the particular disagreement or establish its legal merits.
Source: business.gov.au: What to do when you haven't been paid
Make the remaining account easy to follow
In the hypothetical example, send a statement that shows the first invoice paid and identifies the second invoice separately. If an allocation question remains, explain it plainly rather than hiding the uncertainty in a single balance. Avoid saying that the customer admitted every amount unless a lawyer has assessed a proper basis for that statement from the actual evidence.
Choose the response to the real issue
If the second invoice involves a genuine dispute, address it through the appropriate clarification or dispute process. If the customer accepts it but cannot pay, the discussion is different. Keep those positions distinct in the collection notes. Do not apply a standard demand sequence without considering the response already received and any relevant contractual requirements.
Use accurate records for the next decision
Retain the payment allocation, dispute explanation and supporting documents together. CRP can help review the commercial recovery options for the unresolved amount. The aim is to pursue the correct balance on its own evidence, while giving the customer proper credit for the payment made and avoiding unsupported claims about what that payment proves.