Switching payroll provider after STP or super errors

Payroll provider missed STP reports or paid super late? Fix the errors first, then switch without duplicate income statements or late Payday Super contributions.

By SoftwareHQ Editorial Team — Updated

Who this is forAustralian employers whose payroll software or payroll service has missed STP reports, reported wrong amounts or paid super late, and who want to move to another provider.

In short

  • Fix the errors before you move, while you still have access to the software that made them. The super deadline does not move when a provider’s processing is delayed, and the super guarantee charge is assessed on the employer. Source: ATO · ATO
  • Under Payday Super, each contribution must be received by the employee’s fund within 7 business days after payday. Source: ATO
  • Switch on 1 July if you can. A mid-year switch works if you move year-to-date totals with one of the ATO’s methods. Otherwise employees see duplicate income statements. Source: ATO
  • Keep pay slips going within 1 working day of each payday during the change, and keep time and wages records for 7 years. Source: Fair Work · Fair Work

1. Fix what went wrong first

Correct current errors in the software that made them, while you still have access to it. The obligations stay with you as the employer, whichever product you use.

ProblemWhat to do
Super for a payday reached the fund late, or not at allPay the outstanding amount to the employee’s fund now. A part payment still reduces the charge. Keep a record of what went wrong and how you fixed it.The fund must receive it within 7 business days after payday, or 20 for a new employee’s first contribution or a first payment to a new fund. An error or delay in processing does not extend this. Source: ATO · ATO · ATO
An STP report wasn’t lodged on paydayLodge it now. The ATO’s correction rules cover wrong amounts, not a report that was never lodged.STP reports are due on or before each payday. Source: ATO · ATO
Employee year-to-date amounts in STP are wrongSend the correction within 14 days of finding the error, or in the next regular pay event in the same financial year.An uncorrected report can attract a penalty for a false or misleading statement. Source: ATO
PAYG withholding totals were reported too high or too lowRevise the activity statement for that period, or carry the correction forward to the current period. Record the choice in writing.Carrying forward an amount you under-reported is capped at $2,500 for small withholders. Source: ATO
Qualifying earnings or super liability missing from STP (paydays from 1 July 2026)Ask the provider when its product will report both. Keep your own super guarantee records for each payday until it does, then report year-to-date amounts as soon as you can.The ATO accepts ordinary time earnings until 30 June 2027. From 1 July 2027 it rejects reports without both amounts. Source: ATO
Child support amounts reported too highGet authorisation from the Child Support Registrar before you lodge a correction that reduces the amount.Special rules apply to child support corrections. Act as soon as you find the error. Source: ATO
Wages underpaid because pay rates or award rules were set up wrongPay the shortfall as soon as possible, in the next pay or as a separate payment. If you can’t pay it at once, agree a written payment plan with the employee.Record the back payment in the employee’s pay records. Super on a back payment is due within 7 business days after the employee’s next regular payday. Source: Fair Work · ATO
Data you already finalised was wrongLodge an update event as soon as possible, tell the employee, and revise W1 and W2 on the activity statement for that period.Finalised STP data can be amended for up to 5 years after the end of the financial year. Source: ATO

If super was late

  • For paydays from 1 July 2026 you no longer lodge a super guarantee statement. The ATO calculates the super guarantee charge for each payday and sends a notice of assessment. Source: ATO
  • The charge has four parts: the unpaid super, notional earnings (interest), an administrative uplift of up to 60% of those two amounts, and a choice loading if you paid the wrong fund. Source: ATO · ATO
  • Paying the fund before an assessment reduces the charge. You can also lodge a voluntary disclosure statement before an assessment arrives, which can also reduce it. Source: ATO · ATO
  • From 1 July 2026 to 30 June 2027 the ATO rates behaviour under PCG 2026/1. Low risk means you tried to pay each payday and fixed any gap as soon as reasonably practicable; there is no further review. Medium risk means you fixed it within 28 days after the end of the quarter the wages were paid in. Anything later is high risk. Source: ATO

2. Decide whether to switch

You can change payroll solution at any time, subject to your contract. Source: ATO

Signs the product is the problem:

  • Super keeps reaching funds late because of the provider’s processing time.
  • You hear about failed STP lodgements from the ATO or your employees, not from the software.
  • The product can’t report qualifying earnings and super liability for Payday Super.
  • Support can’t tell you what went wrong or how to correct it.
  • There is no way to send an update event, so you can’t correct year-to-date data.

3. Pick the switch date

1 July

Nothing to carry over. Start the new software with zero year-to-date amounts. Finalise the old software for the previous year by 14 July, so check you’ll still have access until then. Source: ATO · ATO

Mid-year

Pick a year-to-date method from step 4 before the first pay run in the new software. Switch straight after a pay run whose super has been received by every fund, so no contribution is in transit between systems. Source: ATO · ATO

4. Move year-to-date totals without duplicate income statements

The ATO shows a separate income statement for each combination of ABN, branch, BMS ID (the identifier of the payroll software that lodged the report) and employee Payroll ID. New software means a new BMS ID and usually new Payroll IDs. Source: ATO

The common mistakeEntering year-to-date totals in the new software without zeroing out the old software or reporting the previous BMS ID. Employees then see duplicate income statements, and you report more PAYG withholding than you owe.

Replacement

Result: One income statement per employee.
Use it when: The new software supports it and you know the previous BMS ID or employees’ previous Payroll IDs. It works without access to the old software.
What to do: Enter the year-to-date totals in the new software, then send an update event that includes the previous BMS ID or Payroll IDs. They can’t go in a pay event.

Zeroing out

Result: One income statement per employee.
Use it when: The old software offers it and you still have access.
What to do: Before moving any totals, send an update event from the old software showing every year-to-date amount as zero. Then enter the totals in the new software and lodge an STP report.

Same BMS ID

Result: One income statement per employee.
Use it when: The new software lets you nominate a BMS ID and you use the old one.
What to do: No need to tell the ATO, because the ABN, branch and BMS ID combination hasn’t changed. If an employee’s Payroll ID changes, you still need to report that.

Start from zero

Result: Two income statements per employee for the year.
Use it when: You don’t move year-to-date totals.
What to do: No need to tell the ATO. Finalise the old and new records by 14 July. If you might lose access to the old software, or the old ABN or branch will be cancelled, finalise the old records when you switch.

If none of these fit, the ATO asks you to phone 13 28 66. Source: ATO

5. Cut over super payments

  1. Before the last pay run in the old software, check how long its super payments take to reach funds. That time counts inside the 7 business days. Source: ATO
  2. After that pay run, confirm every fund received the contribution. Sent is not received. Source: ATO
  3. Set up super payments in the new software before its first payday: its built-in payment option, a commercial clearing house, or your default fund’s payment option. The ATO’s Small Business Superannuation Clearing House closed on 1 July 2026. Source: ATO
  4. Check each employee’s fund details, including the fund ABN or USI and member number. A contribution is only on time if the fund receives it with the details it needs to allocate it. Source: ATO
  5. Changing software doesn’t give you extra time. The 20 business day allowance covers a new employee’s first contribution and a first payment to a new fund. A software change isn’t on the list. Source: ATO
  6. If you move year-to-date totals, include qualifying earnings and super liability. STP reports both as year-to-date amounts. Source: ATO

6. Move the data

  • Employee details: name, address, date of birth, tax file number declaration details, bank accounts and employment type.
  • Pay setup: pay rates, award or enterprise agreement classification, allowances and pay frequency.
  • Super: each employee’s fund, fund ABN or USI, member number, and any salary sacrifice arrangements. Source: ATO
  • Leave balances at the switch date: annual, personal/carer’s and long service leave.
  • Deductions: union fees (STP deduction type F), workplace giving (type W) and child support, with the Services Australia notices. Source: ATO
  • Year-to-date totals if you are moving them (step 4), checked against the last STP report from the old software. Source: ATO
  • Records: pay slips, pay history, STP lodgement history and super payment confirmations. Time and wages records must be kept for 7 years. Source: Fair Work

7. Before you cancel the old provider

  • Export everything in step 6, and check how long you keep access after cancelling. Source: Fair Work
  • Send the zero-out update event if you chose that method. Source: ATO
  • Finalise the old records now if you won’t have access on 14 July. Source: ATO
  • Confirm the last super payment from the old software reached every fund. Source: ATO
  • Check the notice period in your contract. The ATO lets you change payroll solution subject to your contractual arrangements. Source: ATO
  • Keep pay slips going within 1 working day of each payday during the change. Source: Fair Work

Questions to ask a new payroll provider

  • How will I know if an STP lodgement fails, and how quickly?
  • How do you pay super, and how many business days does it take to reach funds?
  • Can I report my previous BMS ID and Payroll IDs, or do I need to zero out in my old software?
  • Can I import year-to-date totals, including qualifying earnings and super liability?
  • Do you handle union fee, workplace giving and child support deductions, and report them in STP?
  • Is phone support included on my plan?
  • Does your employee app show my staff offers or financial products, and can I turn that off?
  • If your system causes a late super payment or a wrong STP report, what do your terms say you will cover?
  • How do I export all my records if I leave?

What each payroll product documents for switching

From each vendor’s own help pages, checked 26 Sep 2026. “Not documented” means we could not find it, not that the product can’t do it. Confirm the method with both vendors before your first pay run.

Xero

Moving in: Replacement: the migration filing tool reports your previous BMS ID and each employee’s previous Payroll ID.
Moving out: Not documented for leaving. An STP reset tool that sends $0.00 year-to-date amounts is documented for a wrong ABN or branch.
Year-to-date totals are entered as opening balances for each employee.Vendor pages: Report previous payroll information · Update your ABN or branch number for STP

Payroller

Moving in: Replacement: the ‘Migrate STP Report’ feature reports your previous BMS ID and each employee’s previous Payroll ID.
Moving out: Not documented for leaving. Zeroing figures with negative amounts is documented for an ABN change.
Year-to-date totals go in as opening balances with an ‘as at’ date. The ABN and branch must match the previous software.Vendor pages: Transfer STP to Payroller (1 Nov 2023) · Changing ABN (26 Nov 2021)

MYOB

Moving in: Replacement, BMS ID only: report the previous BMS ID when you set up STP. The ATO must accept it before you can process pays. Previous Payroll IDs are not documented.
Moving out: Not documented.
Pay amounts for the year so far are entered by hand in each employee’s pay history. MYOB’s free migration through MMC Convert moves transactions as general journals, not through MYOB payroll.Vendor pages: Notify the ATO for STP reporting · Pay history for the current year · Moving to MYOB

Reckon One

Moving in: Replacement, BMS ID only: send an update event with the previous BMS ID and keep each employee’s number from the old software. Or zero out in the old software first.
Moving out: Documented: lodge a finalisation with every value replaced by $0.00 when you move from Reckon One to other software.
Year-to-date totals are entered as initial YTDs for each employee. Free migration, including payroll year-to-date balances for up to 10 employees from Xero or MYOB, applies to Reckon Payroll Plus and Premium plans.Vendor pages: Adding your previous BMS ID (16 Dec 2024) · Zeroing out method (29 May 2025) · Assigning YTD values (5 Nov 2025) · Free data migration (1 Sep 2026)

Employment Hero

Moving in: Same BMS ID: enter the old software’s BMS ID and copy each employee’s Payroll ID. Or zero out in the old software first.
Moving out: A $0 earnings reset event is documented for fixing wrong business or employee details, not for leaving.
Year-to-date totals are imported through Opening Balances. Switching in requires a paid implementation service: guided $500–$750, or managed from $100 per employee.Vendor pages: STP transition options (31 Aug 2026) · Earnings reset event (31 Aug 2026) · Payroll implementation

KeyPay

Moving in: Same BMS ID: enter the old software’s BMS ID and copy each employee’s Payroll ID. Or zero out in the old software first.
Moving out: A $0 earnings reset event is documented for fixing wrong business or employee details, not for leaving.
Same help content as Employment Hero Payroll. Year-to-date totals go in as opening balances.Vendor pages: STP transition options (31 Aug 2026) · Earnings reset event (31 Aug 2026)

QuickBooks Online

Moving in: Same BMS ID: enter the old software’s BMS ID and copy each employee’s Payroll ID. Or zero out in the old software first.
Moving out: A $0 earnings reset event is documented for fixing wrong business or employee details, not for leaving.
QuickBooks Payroll is powered by Employment Hero and its help content is sourced from Employment Hero. Year-to-date totals go in as opening balances.Vendor pages: STP transition options (26 Mar 2026) · STP reset event (11 Jun 2026)

Compare prices, STP and Payday Super claims, and support in the payroll software comparison.

Sources

Checked 26 Sep 2026. Dates are the ones printed on each page.

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