Best Payroll Software for Accountants in Australia (2026)

If you are an accountant, bookkeeper or BAS agent who runs payroll for client businesses, you are choosing software for a book of clients rather than for one business. The software has to lodge Single Touch Payroll for every client on every payday, pay super fast enough for Payday Super, apply the right Modern Award, and let your practice manage many client files without a separate login for each. In most practices the choice is made client by client, starting from the ledger each client already uses.

How we chose. We list 10 payroll tools for Australian businesses and cost each through the same engine as the payroll software comparison. For client payroll we weighted four things: STP Phase 2 and Payday Super readiness, award interpretation, how the payroll connects to the ledger you keep for the client, and what the vendor offers a practice. Our database does not record multi-client or practice features, so every practice-program fact on this page comes from the vendor's own partner page, linked where it appears. Deel, Remote, Papaya Global and Payoneer Workforce Management are left out of the picks because they are built to employ and pay people overseas; our guide to payroll for global teams covers them. Rippling and Sage are left out because our data has no published Australian payroll price for either, so the table cannot cost them. The table above opens at 10 employees; enter each client's headcount and it re-prices. Affiliate status never changes the picks or their order.

What an Australian practice needs from client payroll software

An Australian accountant or bookkeeper running client payroll needs software that lodges STP Phase 2 on every pay run, for every client, because that report now carries super as well as pay. Beyond STP Phase 2 it needs Payday Super handling, award interpretation that matches each client's staff, and a practice view that opens every client file from one login. The first three are features of the payroll product; the fourth comes from the vendor's practice or partner program.

For the first three, here is what our data records for each of the four picks:

"Payday Super ready" is the vendor's own statement that its product handles super paid with each pay run; we have not run a pay run to test it.

The "Connects to" column is the one that shapes a practice's choice. Xero, MYOB and QuickBooks Online run payroll inside their own ledger, so a client's pay run posts to the books with nothing to map. Employment Hero is a separate payroll and HR system that posts to any of those three, which lets a practice with a mixed client book run one payroll across ledgers.

Can a bookkeeper or BAS agent run payroll for clients?

A bookkeeper can run client payroll for a fee only as a registered BAS agent; working under a registered agent's supervision covers data entry, not running the payroll. The Tax Practitioners Board's guide to BAS services lists providing a payroll service that reports employee payroll information through STP-enabled software, working out PAYG withholding, calculating leave payments and dealing with super paid through a clearing house as BAS services. Since 2020 a TPB instrument has also let BAS agents advise on the super guarantee charge and represent clients to the ATO about it.

The same page draws the line on the other side. Transmitting data through STP software where no tax law has to be interpreted, data entry under a registered agent's instruction and supervision, and bank reconciliations are not BAS services. The TPB says there are significant civil penalties for providing BAS services for a fee while unregistered.

Registration is with the TPB, not the software vendor, though some practice programs below ask about your practice before they give you client tools: Xero's, for example, needs at least one registered accountant in the practice.

Payday Super and STP Phase 2 for client payroll from 1 July 2026

Payday Super changed client payroll from 1 July 2026: employers now pay super guarantee for each payday instead of each quarter, and the ATO says a contribution is on time only if the employee's fund receives it within 7 business days after payday, with 20 business days for a new employee's or new fund's first contribution. For a practice, every pay run is now a super deadline.

Three changes from the ATO's changeover guidance land on whoever runs the pay run:

• The Small Business Superannuation Clearing House has closed. Clients who used it need another route to pay super, usually the clearing house built into their payroll software or one the software connects to. Allow for that provider's processing time inside the 7 business days.
• STP now carries super. For paydays from 1 July 2026, each employee's year-to-date qualifying earnings and super liability go in every STP report, so pay codes need mapping to qualifying earnings in each client file.
• The grace period for reporting ends on 30 June 2027. Until then the ATO still accepts ordinary time earnings in STP reports; from 1 July 2027 it says it will reject reporting that leaves out qualifying earnings and super liability, and penalties may apply.

The ATO's first-year compliance approach says employers who pay super for each payday on time and fix errors quickly will not be its focus. In practice that means the pay run, the super payment and the STP report go out together, which is easiest when one product does all three. Every pick on this page records both STP Phase 2 and Payday Super readiness in the table above.

Award interpretation across a client book

Award interpretation decides how much checking a practice does on each pay run. Software that reads timesheets and applies the right Modern Award's penalty rates, overtime and casual loading lets you run a hospitality or retail client's payroll without checking every line against the award. Our data records it in several different ways, so here it is for every payroll provider we list, with the wording intact:

"Yes" means the software applies award rules from timesheets. "EH engine" at QuickBooks means its payroll runs on Employment Hero's interpretation engine. "Via integration" at MYOB means award rules come from a connected workforce-management app rather than MYOB itself. "Limited" means some award pay items are loaded but you decide which rate applies to which hour. "No" and "Not stated" mean the vendor does not do it or does not say.

For a practice, this column often matters more than price in deciding where each client goes. A professional-services client on salaries can sit on any of the ledgers' own payroll; a café with weekend casuals is safer on an engine that interprets the award. Our guide to payroll software for award interpretation compares the engines in more depth, for a single business rather than a client book.

Practice programs for Xero Payroll, MYOB, Employment Hero and QuickBooks

Each of the four picks has a program for accounting and bookkeeping practices, and they differ in who bills the client. Xero and QuickBooks bill the client and give the practice tools to manage every client file. MYOB lets the practice pay for client subscriptions itself. Employment Hero's Certified Partner program lets the practice resell payroll under its own billing. All of this comes from the vendors' own pages, read on 18 October 2026.

Xero. The Xero Partner Program is free with no ongoing costs. It asks for an accounting practice with at least one registered accountant and one staff member who completes Xero advisor certification within 30 days. Partners get a free Xero subscription to run the practice and Xero Partner Hub for the client portfolio, and Bronze status and above is eligible for discounts on Xero business edition subscriptions.

MYOB. The MYOB Partner Program includes free access to MYOB Practice Compliance for managing client files and one free MYOB Business Pro subscription, which covers the practice's own payroll. A practice chooses Partner Pays, where it pays for client subscriptions, or Client Pays. On MYOB Business sold to clients it takes either a wholesale discount, 15% to 30%, or a commission, 10% to 17.5%, rising with the status credits it earns from referrals and retained subscriptions.

Employment Hero. Employment Hero runs two partner models. A Referral Partner introduces clients for a commission and Employment Hero bills, implements and supports them. A Certified Partner completes Employment Hero's certification, buys at wholesale rates, bills clients directly, sets its own margin and acts as their first-line support. Employment Hero names accountants and outsourced payroll firms among the businesses the Certified program is for, and says new Certified Partners typically start on the referral program first. Wholesale rates are set in each partner's agreement and are not published.

QuickBooks. Intuit's page for accountants and bookkeepers describes Intuit Accountant Suite, which puts all of a practice's QuickBooks client files under one sign-in, and partner access to QuickBooks Online Advanced, QuickBooks Time and a free QuickBooks Payroll subscription for the firm. Intuit says ProPartner Accountants will succeed the ProAdvisor program in early 2027, so check what a new partner joins.

Prices in the table are each vendor's published monthly figure in Australian dollars; we do not add or remove GST, and partner discounts are not applied. Plans and pricing checked October 2026.

How client headcount changes the payroll bill

Payroll pricing is built differently at each pick, so the same client can cost different amounts on each depending on its headcount. Run each client's employee count through the table above rather than reading one figure across the book; the four pricing shapes are:

• Xero charges by plan rather than per employee until the top of its plan ladder: the client's payroll headcount picks the Xero plan, and each higher plan covers more people. The table prices the plan that covers your number.
• MYOB sells a standalone plan, $15/mo (Payroll Only, up to 4 emp), with a hard cap; above it, payroll moves to a Business plan at $3/emp on Lite/Pro.
• Employment Hero charges $10/emp/mo (Payroll) but sets a monthly minimum, so small clients all pay the same floor; the table applies it at your headcount.
• QuickBooks Payroll charges $6/emp/mo on top of a QuickBooks Online plan, $33/mo (Simple Start) in our table.

For a practice paying client subscriptions through a partner program, these are list prices before any wholesale discount. For a client already paying for Xero, MYOB Business or QuickBooks Online accounting, the extra cost of payroll is smaller than the table's full figure, because the table counts the accounting plan that payroll needs.

Which payroll software for accountants, by client ledger

Choose client by client, starting from where the books are kept:

• The client's books are in Xero and its staff are salaried or on a simple award: Xero Payroll, because the plan they already pay for may cover their headcount.
• The client is small, on MYOB, or you want to pay for its subscription through your practice: MYOB, through Partner Pays.
• The client has rostered or casual staff on a Modern Award, or you want one payroll across clients on different ledgers: Employment Hero, through referral or, if you want to bill payroll as your own service, as a Certified Partner.
• The client's books are in QuickBooks Online: QuickBooks Payroll, which our data lists with award interpretation on Employment Hero's engine.

Whichever you choose, set each client file up for Payday Super before its next pay run: map qualifying earnings in STP, and confirm the clearing house gets super to each fund inside the 7 business days.