After the super clearing house closed: check your payment trail
Start with the changeover records
The Small Business Superannuation Clearing House closed on 1 July 2026. Businesses that used it needed another way to pay employee super. If the changeover was rushed, an instruction in the old system and a payment in the new one may be difficult to match.
Start by listing the payments you expected to make around the changeover. Record the employee, period, amount, payment date and provider used. Separate what the payroll records say was due from what the payment records show was sent.
Do not treat a missing receipt as proof that nothing was paid, or a bank debit as proof that every employee's contribution reached the correct fund. Identify the gap and check it with the provider before deciding what needs correcting.
Trace each unresolved payment
For each entry you cannot reconcile, gather the transaction reference, bank record and any confirmation or rejection message. Check whether the payment was allocated, returned or remains unresolved. A total paid to a provider may need to be checked against several employee contributions.
Ask the provider or fund for confirmation of the relevant payment status and the information needed to resolve any discrepancy. Check employee details and fund information against your records instead of repeatedly resubmitting the same instruction.
Keep a note of who you contacted, what they confirmed and the next action agreed. This gives the payroll team and your adviser one payment trail to work from. It can also help avoid a duplicate payment while an earlier transaction is being traced.
Source: ATO: How to transition from the Small Business Superannuation Clearing House
Separate earlier periods from current obligations
The clearing house closure coincided with the move to Payday Super from 1 July 2026. An unresolved contribution for an earlier quarterly period and a contribution connected with a later payday should not be treated as though they automatically follow identical rules.
Give your registered tax agent or accountant the period and payment dates for each unresolved item. Ask them to establish which rules apply, whether a shortfall exists and what reporting or payment is required. Do not calculate the result from an old example without checking its period.
Continue checking current payroll obligations while the earlier payments are reconciled. A change of payment provider does not itself settle an unpaid contribution or determine whether a charge applies.
Source: ATO: Payday Super for employers
Check the replacement process
If your replacement payment method is not working reliably, review it with your payroll provider. Your existing software may include a suitable super payment function. Other options may be available through a commercial clearing house or a super fund.
Ask how the service confirms successful payments, flags rejected contributions and handles corrections. Confirm who in your business checks those messages and follows up unresolved items. Sending an instruction should not be the last step in your internal process.
Keep the provider's current processing guidance with your payroll checklist. Allow for the time needed to identify and resolve errors when planning payments, and check the applicable deadlines with your adviser.
Prepare a clear handover for your adviser
Bring the reconciled payment list, payroll reports, provider responses, fund confirmations and any ATO correspondence to your adviser. Mark which facts are confirmed and which questions remain open. This is more useful than a single estimated total with no supporting trail.
If contributions were missed or late, ask what needs to be corrected and when. Do not assume that switching systems, sending a replacement payment or contacting the ATO resolves every reporting requirement.
Agree who will make each correction and how completion will be checked. Keep the unresolved items visible until the relevant confirmation has arrived, so they are not lost between the payroll team, the provider and the adviser.