Super Clearing House Options for Employer Clients

A super clearing house replacement must get each employer client’s contributions to the right funds on time. The ATO’s Small Business Superannuation Clearing House has closed. Choose a payroll-linked service or a separate clearing house, then reconcile the old payments before switching.

The ATO Super Clearing House Has Closed: What That Means

The Australian Taxation Office (ATO) clearing house no longer accepts payments, registrations or access to historical records. It stopped new registrations before its permanent closure. The ATO’s closure guidance explains the applicable boundaries.

The free Small Business Superannuation Clearing House served registered employers with 19 or fewer employees, or annual aggregated turnover below $10 million. Employers sent one payment and instructions for distribution to employees’ funds. Eligibility for that service does not establish eligibility for a replacement.

You cannot sign back in to download old payment records. Start with the transaction history the employer downloaded, your practice’s saved copies and bank records. Match these to fund receipts and any refund notices. If records are missing, contact the ATO about the specific payment. A bank debit alone cannot prove that every fund received its contribution.

Payments received by the old clearing house after closure are returned within seven business days. For a rejected contribution, establish whether the money reached the fund, returned to the employer or remains unresolved. Correct the employee’s details before paying through the new service. Assess any late-payment obligations under the rules for that payment period.

What a Super Clearing House Does for an Employer

A super clearing house takes the employer’s payment and contribution instructions, then distributes the amounts and SuperStream data to each employee’s fund. For example, one payroll batch can cover employees in several industry funds and a self-managed super fund (SMSF).

Under Payday Super, funds generally must receive contributions within seven business days after payday. Receipt requires the money and the information needed to allocate it. An approval in payroll or a debit from the employer’s account is an earlier step. The ATO’s Payday Super guidance owns exceptions and the commencement boundary.

Allow for authorisation, bank clearing and the clearing house’s distribution time inside that window. The Payday Super checklist covers the broader calculation and reporting changes.

The clearing house does not choose the employee’s fund for the employer. A successful data check also does not establish that the employer followed the choice and stapled-fund rules. Use the new employee forms guide when collecting a starter’s fund details.

Replacement Options: Payroll Software, Fund Clearing Houses and Commercial Services

Start with the payroll software the employer already uses. Xero, MYOB, QuickBooks and Reckon have payroll-linked super payment routes, though their products and payment partners differ. A separate service suits an employer whose payroll exports a contribution file or whose authoriser works outside payroll.

Fund-arranged clearing houses can pay contributions to other funds as well as their own. AustralianSuper, Aware Super and Colonial First State have employer payment services. Free access depends on the specific employer arrangement. A default-fund relationship can be a condition, but it is not a universal rule across providers.

Commercial operators include SuperChoice and ClickSuper, which also support services distributed through other brands. Beam is another clearing house used inside payroll products. QuickSuper is Westpac’s clearing house and is used through participating fund arrangements. Comparing these names as if every one were a standalone subscription would hide how the employer actually gets access.

Compare the employer’s eligibility and the full cost of its chosen route. A paid arrangement can include file handling, payment reporting or service support. Do not assume an extra fee buys faster fund receipt. The payment method and the actual service terms determine that.

Xero, MYOB and QuickBooks Super Payments

Xero’s auto super uses SuperChoice to distribute contributions. After the pay run, create the super batch and send it to an authorised person for approval. Xero says contributions typically reach funds within four business days. Approval after its 4 pm AEST banking cut-off moves direct debit processing to the next business day.

Xero’s Superannuation Payments report records successful fund crediting in its Sent To Fund column. A manually recorded external payment does not create that evidence. Retain the report when reconciling the first replacement batch.

MYOB’s Pay Super also uses SuperChoice. Its payment guidance describes typical processing of three to five business days, subject to the authoriser and banking steps. The published enterprise guidance gives a 4 pm AEDT direct debit cut-off. Use the guidance for the client’s specific MYOB product when scheduling approvals.

QuickBooks Online Payroll powered by Employment Hero now has HeroClear as well as Beam. Its current help guide describes HeroClear’s real-time payment route and fund checks. Beam remains available with direct debit, electronic funds transfer (EFT) or BPAY. Enabling a clearing house is separate from preparing a pay run.

Reckon One supports Beam batches directly from a paid pay run. Reckon Accounts Hosted uses a different route: its exported SuperStream Alternative File Format (SAFF) file goes to a separate clearing house. Do not promise the Reckon One integration to a Hosted client.

Beam states that direct debit amounts are sent to funds within five business days. EFT and BPAY amounts are sent within three business days after Beam receives both the correct payment and contribution details. These are distribution timings, so include the bank transfer time before Beam receives an EFT payment.

A late-week approval can leave too little time if the employer has already waited several days after payday. Weekends do not consume business days, but they can postpone the start of processing. Authorise with the pay run and monitor errors promptly instead of using the statutory deadline as the submission date.

Fund-Run Clearing Houses: AustralianSuper, Aware Super and Others

AustralianSuper’s Employer Portal replaces its QuickSuper arrangement and uses Wrkr’s clearing house service. Registered AustralianSuper employers can use the portal at no cost. Its transition guidance describes phased movement of QuickSuper accounts to read-only access. Existing employers must follow their own transition instructions before choosing where to lodge the next contribution.

AustralianSuper’s clearing house pays employees’ other funds too. Aware Super also describes contributions to employees across funds, subject to eligibility. Treat the employer’s accepted arrangement as the basis for access. The fund’s employer registration and the clearing house registration can be separate steps.

Colonial First State’s FirstChoice Employer Super Clearing House uses SuperChoice and supports SMSF details. Access depends on how the employer joined CFS. Its payment options include direct debit and direct credit, with no BPAY option. CFS describes direct debit fund receipt in approximately five to six business days.

Before committing a client to a fund-arranged service, record the eligibility condition, any fee basis, payment methods and SMSF support. Include the payroll file format and the employer’s approval permissions. Free clearing house access never gives the employer permission to move an employee from their chosen fund.

Register the correct employing entity, then appoint the business’s payment authoriser and a backup. Give the agent only the access needed for preparation and reconciliation. The employer must understand who can release money from its bank account.

Choosing the Right Clearing House for Each Employer Client

Choose the route that fits the client’s payroll and approval routine, with enough time for contributions to reach funds. Use the same questions for every client instead of prescribing one provider across your whole practice.

Client Factor	Payroll-Linked Route	Separate Clearing House
Payroll software	Direct batch creation when the product supports it	Accepted export format or manual entry required
Employee count	Match the payroll plan and entity limits	Match upload capacity and employer access terms
Pay frequency	Approve super with each pay run	Schedule each upload and payment beside payroll
Processing time	Include authoriser delay and payment-partner time	Include file upload, bank transfer and distribution time
Cost	Assess included access and any extra charges	Assess eligibility for free access or commercial fees
SMSF members	Record the SMSF fields and resolve rejected details	Confirm SMSF registration and payment handling
Payment ownership	Payroll user prepares, authorised business user approves	Define who uploads, pays and monitors refunds

For an SMSF, collect its Australian Business Number (ABN), electronic service address (ESA) and bank account details. The ESA is a SuperStream messaging address, not an ordinary email address. Match the details to the employee’s evidence and resolve any fund-status error before payment.

An ordinary fund’s Unique Superannuation Identifier (USI) identifies the receiving fund product. An SMSF requires its own ABN and payment details. Do not enter the employee’s personal bank account as the SMSF account.

Consider a fictional employer with eight employees paid weekly, including one SMSF member. If its payroll creates a usable batch, integrated payment removes a separate upload each week. If the business’s bank authoriser cannot use payroll, a separate portal can fit better. Either choice still needs a named approver and receipt monitoring after each pay run.

Moving a Client Across: Switch-Over Steps for the Agent

Move the client only after you can distinguish paid contributions from refunds and outstanding amounts. Keep a written switch record for the employing entity, not just a note that a new account exists.

1. Collect employee fund details. Record each fund name, USI or SMSF ABN, member number and the SMSF’s ESA and bank details. Resolve missing or changed details with the employee.
2. Reconcile the old service. Match each employee’s last contribution to payroll, the clearing house history and fund evidence. Record refunded amounts separately from contributions without receipt evidence. Investigate an unresolved payment before duplicating it.
3. Register the employer. Use its legal entity details and correct bank account. Accept the service terms, complete payment authority and appoint the authoriser with a backup.
4. Prepare the first batch. Select the intended pay run or contribution period and compare employee totals with payroll. Confirm that contributions already paid through the old service are excluded.
5. Obtain approval and payment. Tell the authoriser when approval must happen and ensure the account has sufficient funds. For EFT or BPAY, use the batch’s exact payment reference and amount.
6. Verify receipt and handle failures. Confirm the distribution result for every employee and retain the receipt report. If a payment is returned, read the error, correct the underlying details and resubmit the affected contribution. Assess whether the original deadline has been missed.
7. Confirm the new routine in writing. Record the service, first pay run covered, approval time, payment method and who monitors returns. Ask the employer to acknowledge its approval responsibility.

A successful switch has one recorded contribution per employee for each covered pay run, no unexplained old-service balance and a working approval routine. A debit without matching fund evidence leaves the reconciliation open. If a payment remains unresolved, escalate with the batch reference and bank evidence before sending a duplicate.

New employer clients go straight onto a supported service during onboarding. Collect their payroll and fund details through the bookkeeping client onboarding checklist. Keep super reconciliation separate from Single Touch Payroll finalisation: finalising payroll reports does not establish that contributions reached funds.