MYOB Acumatica Payroll: STP Phase 2, Payday Super and the 12% Super Guarantee for 2026-27

Updated 20 October 2026: rebuilt for the 2026-27 year now that Payday Super is live. New short answer, At a glance block, question headings, a before-and-after table, re-verified ATO and MYOB sources (super guarantee table, Payday Super deadlines, MYOB Acumatica 2025.2.100 release notes), and the FAQ moved to the live FAQ block.

MYOB Acumatica Payroll (formerly MYOB Advanced Payroll) lodges Single Touch Payroll (STP) Phase 2 automatically when each pay run completes, applies the 12% super guarantee, and from 1 July 2026 flags qualifying earnings and builds a super batch after every pay so contributions reach funds within 7 business days under Payday Super. Version 2025.2.100 or later carries the Payday Super changes.

At a glance

• Who it is for: Australian employers running payroll inside MYOB Acumatica, or MYOB Acumatica Payroll on its own, with enough staff, awards or entities that a small-business payroll tool no longer fits
• Problem it solves: STP Phase 2 lodgement, Payday Super timing and super guarantee calculation in the same system as the general ledger, with no export and import between payroll and accounts
• Platforms: MYOB Acumatica Payroll (Australia), standalone or integrated with MYOB Acumatica ERP
• Typical cost: MYOB prices per named user and quotes through partners; indicative subscription and implementation ranges, AUD ex GST, are in our MYOB Acumatica cost guide
• Typical timeline: a finance-only MYOB Acumatica implementation runs 2 to 3 months in our cost guide; a payroll cutover is scheduled to a pay-period start inside that window
• Last verified: 20 October 2026 against the ATO super guarantee percentage table (updated 17 April 2026), the ATO Payday Super payment deadlines (updated 29 September 2026) and the MYOB Acumatica 2025.2.100 Payday Super release notes

The 2026-27 payroll year is the first full year under Payday Super, and it’s also the year the maximum contribution base went annual and the 15% tax bracket arrived. If you run MYOB Acumatica Payroll, most of that is handled by the software once you’re on a current version. The parts that aren’t handled for you are the pay item flags, the super batch rhythm and the clearing house timing, and those are what this guide walks through.

What does MYOB Acumatica Payroll cover?

MYOB Acumatica Payroll is MYOB’s payroll product for medium and large Australian employers. MYOB’s product page lists STP and SuperStream, digital timesheets, time and attendance on a mobile app, rostering, onboarding workflows and employee self-service for payslips, leave and personal details, and says the product always uses the latest tax rates. It runs on its own or with MYOB Acumatica, where it’s the same platform and the same login as your financials.

That last point is the practical reason mid-market businesses choose it. Payroll journals post to the general ledger in the same system, so wages expense, PAYG withholding and the super liability land in the right accounts on the pay date and nobody reconciles a payroll export against the accounts at month end. Leave accruals, award rates, Employment Termination Payments and PAYG withholding are all handled inside the pay run. If you’d like to see what that looks like for your entity structure, we’re a MYOB Acumatica partner in Brisbane (listed on MYOB’s partner directory) and we’ll walk through it with you.

Is MYOB Acumatica Payroll STP Phase 2 compliant?

Yes. STP Phase 2 replaced the single gross figure with a disaggregated one. The ATO’s STP Phase 2 reporting guidelines (updated 12 November 2025) require gross, paid leave, allowances, overtime, bonuses and commissions, directors’ fees, lump sum W and salary sacrifice to be reported as separate amounts, with paid leave broken down further by type. The ATO uses that detail to pre-fill tax returns and to work out whether super has been paid on the right base.

In MYOB Acumatica Payroll the mapping happens once, on each pay item, and then every pay run reports it. The categories you’ll see on the Pay Item Liabilities form include qualifying earnings (Q), super guarantee liability (L), reportable employer super contributions (RESC), super sacrifice (S), other benefits sacrifice (O) and the STP allowance categories (car, laundry, meals, other, transport and travel). MYOB’s Single Touch Payroll help covers each category and notes that once STP is set up you no longer produce payment summaries, and you only lodge a TFN declaration if you haven’t yet moved to Phase 2.

How STP Phase 2 reporting works in each pay run

When a pay run completes, MYOB Acumatica Payroll creates an STP batch and submits it to the ATO after you accept the declaration that the data is correct and you’re authorised to send it. There’s no separate lodgement tool. The batch sits on the Manage STP Submissions form (MPPP5019) with a status of submission pending, submission received, submission successful, submission not successful (the ATO returned errors) or submission failed (the batch never reached MYOB’s online services). Status is tracked at the batch, branch and employee level, and because the ATO rejects records individually you only correct the employee records that bounced. End of financial year finalisation is lodged from the STP Finalise form (MPPP5023), with an optional preview before you send.

What is the super guarantee rate for 2026-27?

The super guarantee rate is 12% for the year from 1 July 2026 to 30 June 2027, unchanged from 2025-26 and now the permanent rate in the ATO’s super guarantee percentage table (updated 17 April 2026). The table also shows the transitional Norfolk Island rate at 11% for 2026-27, which MYOB Acumatica does not apply automatically; MYOB’s payroll compliance changes page says to override the rate on the employer super pay item for Norfolk Island staff.

What did change on 1 July 2026 is the base and the cap. Super is now calculated on qualifying earnings instead of ordinary time earnings, and the maximum contribution base moved from a quarterly figure to an annual one, which MYOB lists as $270,830 for 2026-27. MYOB Acumatica applies the annual threshold to any pay with a physical pay date on or after 1 July 2026, using the business date to pick the right rule.

What changed under Payday Super on 1 July 2026?

Payday Super replaced the quarterly super guarantee cycle. The ATO’s paying super for your employees guide (published 23 June 2026) puts it plainly: from 1 July 2026 you must pay super so it’s received by the employee’s fund, with enough information to allocate it, within 7 business days after each payday, or you’re liable for the super guarantee charge. The fund then has 3 business days to allocate or reject the payment, and there’s no extension to the 7 business days if a payment is rejected. The Small Business Superannuation Clearing House closed permanently on 1 July 2026, per the ATO’s employer resources page (updated 21 July 2026), which also carries the ATO’s “year 1: getting it right” fact sheet on its first-year compliance approach.

Qualifying earnings replace ordinary time earnings

MYOB Acumatica 2025.2.100 added a Liable for Qualifying Earnings (QE) field to the Pay Item Liabilities form (MPPP1025), linked to the existing Liable for Superannuation (SG) field. New pay items get QE when you tick SG. Existing pay items did not get it retrospectively, which is why MYOB’s Payday Super transition guide (18 May 2026) told customers to review every pay item after the last June pay run and before the first July one, ticking both boxes on everything that counts. MYOB’s qualifying earnings setup page adds the two cases where the flags differ: voluntary super for an under-18 working fewer than 30 hours a week is SG but not QE, and a salary sacrifice deduction item should carry neither flag when the earnings item already holds the full pre-sacrifice amount, otherwise the super calculation is reduced.

From 1 July 2026 the STP batch reports year-to-date qualifying earnings for each employee, stops reporting QE once the annual maximum is reached, and still reports the year-to-date super liability. If the June review was rushed, the post-go-live checks in our Payday Super guide are the place to start, because a wrong flag doesn’t error; it just accrues a shortfall or an overpayment on every pay.

A super batch after every pay run

The operational change is the batch rhythm. MYOB’s release notes say to run Create Superannuation Batch after each pay run and submit it to your clearing house or PaySuper as usual. The same release added an Adjustment Type filter to the Create Super Batch form (MPPP5005), so a negative and positive adjustment pair from a corrected pay is linked and picked up together, and an Adjusted Contribution tab that lists unpaid adjustments from completed pay runs in the 90 days before the batch start date. A fortnightly payroll now means 26 super batches a year instead of four quarterly ones, and the 7 business days run from the payday, not from the day someone gets around to the batch.

The ATO’s payment deadlines page (updated 29 September 2026) gives two concessions worth building into your process. The first contribution for a new employee, or the first to a new fund, must be received within 20 business days after that payday, not 7. And super on an out-of-cycle payment such as a bonus or back pay is due with the next regular payday’s contribution, so the batch for that next run has to pick it up.

We stopped seeing Payday Super as a payroll change about two pay runs in. It’s a treasury change. The payroll team does the same work every fortnight; the person who used to release one super payment a quarter now releases 26, and the cash has to be there each time.

Josh Craig, Director, Auboros

What happens if a contribution lands late?

The ATO’s guide says the most important thing after a missed or short payment is to pay the correct amount to the fund as soon as you can, before any super guarantee charge assessment arrives. The charge still applies to late payments and MYOB’s Payday Super guide notes that the ATO has indicated a practical, education-focused approach to compliance in the first 12 months, which is comfort for teething problems and not a reason to leave the batch until Friday. The ATO now matches STP-reported super liability against what funds receive, so a late batch is visible without an audit.

Other 2026-27 payroll rates MYOB Acumatica applies automatically

MYOB’s payroll compliance changes page lists what the software applies to any pay with a physical pay date of 1 July 2026 or later. No manual adjustment is needed for these:

• PAYG withholding. The 16% bracket became 15% on income from $18,201 to $45,000, with revised resident and non-resident tables.
• Student loans. The compulsory repayment threshold rose from $67,000 to $69,528; the repayment rates are unchanged.
• Employment termination payments. The ETP cap moved from $260,000 to $270,000, the base limit to $13,598 and the per-year-of-service amount to $6,801.
• Medicare levy. The 2% levy is unchanged; the low-income thresholds rose 2.9%.
• Child support. The protected earnings amount for 2026 is $544.88 a week.
• Stapled fund lookups. Mandatory in Flare onboarding from 1 July 2026, which matters if you use MYOB Acumatica onboarding to collect new starters’ fund details.

Government-funded paid parental leave also attracts 12% super for babies born or adopted on or after 1 July 2026, paid by the government to the employee’s fund; it isn’t a MYOB Acumatica setting, but it comes up when employees ask why their payslip shows no super during leave. Leave itself, including accrual rules and the STP leave types, is covered in our MYOB Acumatica leave management guide.

Moving to MYOB Acumatica Payroll from an older MYOB payroll product

MYOB Acumatica Payroll is the product MYOB positions for medium and large employers, and we see most moves into it come from businesses that outgrew a small-business payroll, or that run MYOB Exo Employer Services and want payroll in the same platform as their next ERP. The migration itself is a data job (employees, year-to-date balances, leave balances, pay items and award rules) and a cutover job (last pay in the old system, first pay in the new one, STP finalisation on the old payer record). Scheduling the cutover to a pay-period start keeps the STP year-to-date figures clean. Our MYOB Acumatica support guide covers what support includes after go-live, which for payroll means the twice-yearly compliance releases land in your tenant without a project.

Goes well with

• Payday Super is live: what to check in MYOB Acumatica Payroll now
• MYOB Acumatica EOFY checklist: what to prepare before 30 June
• MYOB Acumatica cost in Australia: licences, implementation and support

Getting MYOB Acumatica Payroll right for 2026-27

We implement and support MYOB Acumatica Payroll for employers across Brisbane, the Gold Coast and the rest of Queensland, including the pay item review, the super batch process and the cutover from an older payroll. If you want a second pair of eyes on your qualifying earnings flags or your 7-business-day process, book a free consultation. We’ll tell you what’s already fine and what needs changing before the next pay run.