Payroll Software a Practice Runs for Its Clients

Payroll software your practice can administer must report through Single Touch Payroll, give staff named access and show every pay run, including runs the client processes. Start with the client’s existing product, reconcile its records and agree who approves, lodges and pays.

Which Payroll Software a Practice Can Administer for a Client

Choose payroll software by the employer file you must operate and the access your practice needs. A client-owned subscription gives you an invited seat. A bureau arrangement lets your practice administer several separate employer files from a shared console.

The employer remains responsible for its payroll obligations under either arrangement. Record the subscription holder, who pays the software provider and how the employer obtains its records when your engagement ends. A practice paying the subscription does not own the employees’ information.

Australian product	Reporting and practice access	Best fit to examine	Handover check
Xero Payroll	Australian STP Phase 2 reporting within Xero. Staff need payroll permissions in each employer organisation.	A client already using Xero with payroll that fits its plan’s employee allowance.	Employee import, opening balances and payroll reports must reconcile.
MYOB Business	STP reporting with mapped pay items. An invited adviser who lodges also registers as a declarer.	An employer already keeping its accounts in MYOB.	Identify the browser or desktop file and its previous BMS identifier.
QuickBooks Online Payroll	Australian payroll powered by Employment Hero, with Phase 2 guidance and accountant access.	A QuickBooks employer needing payroll beside its accounts.	Reconcile payroll categories and the accounts receiving wage and liability entries.
Reckon Payroll	Australian Phase 2 setup and registered-adviser reporting arrangements.	An employer needing a payroll-focused option or already using Reckon.	Confirm the exact product, users and STP sending arrangement.
Employment Hero Payroll	Australian payroll with a partner bureau dashboard and separate employer files.	A practice running several clients, especially where approved hours and awards add complexity.	Check bureau access, employee permissions and each employer’s reporting setup.

Xero, MYOB, QuickBooks and Reckon sell employer products and have adviser arrangements. Their partner programmes do not automatically give your staff payroll access. Employment Hero’s partner arrangement supports a practice bureau. Subscription ownership and billing can sit with the employer or practice where the provider’s agreement permits it.

For a practice administering several employers, Employment Hero Payroll is the strongest fit in this shortlist when bureau access and workforce inputs decide the choice. For straightforward payroll already reconciled in Xero or MYOB, retaining that product can avoid a needless conversion. QuickBooks suits clients already using its Australian accounts and embedded payroll. Reckon deserves a payroll-only comparison where the employer wants to retain a different accounting product.

An employer with one or two staff still needs a reporting method unless an applicable concession changes its obligation. A simple payroll-only product can suit regular pay without buying an accounting package the client does not need. Check the path from draft pay to approval, then demonstrate an error correction. A short setup process cannot compensate for missing Australian reporting or shared logins.

Employee count is only a starting point. Compare a two-person fixed salary employer with a fifteen-person shift employer and a multi-site employer with hundreds of employees. The latter two need closer checks of pay rules, approval levels, bulk imports and report limits. Test the subscribed employee allowance, archived employee treatment and export volume before committing to a larger file.

Standalone payroll sends accounting entries into the client’s accounting product. An accounting payroll module keeps those entries inside the same product. Payroll bundled with invoicing or HR adds employee or commercial records, but those records still need separate permissions and reconciliation.

Use a Pay Run in the Demo

Ask the provider to demonstrate a sample Australian employer file on the computers your staff use. Browser access can support Mac staff without a local installation. A desktop edition needs its own operating-system, hosting and remote-access check.

1. Process ordinary hours with an overtime item and an allowance. Compare the pay components with the employee’s conditions.
2. Change an employee’s pay details and approve leave. Confirm that the history identifies the staff member who changed them.
3. Show the draft report to a separate approver. Test whether that user can approve without editing employee bank details.
4. Inspect the STP output and super payment status. Distinguish an accepted report from money received by a fund.
5. Export pay-run reports, employee balances and a correction history. Confirm the employer can read them after the subscription ends.

Hosted payroll lets authorised remote staff work in the same file. Provider outages can delay access and lodgement, so retain completed reports and an escalation contact. Locally installed payroll needs reliable backups, version updates and a secure way for the adviser to access the file. Neither arrangement makes a shared password acceptable.

Flexibility means adding staff, changing pay frequencies or introducing allowances without losing earlier reports. It also means keeping approval duties separate when a manager starts processing part of payroll.

Separate Country Editions

Sage’s Australian website describes Sage People connecting with local payroll and identifies its own payroll editions for US and UK employees. Those overseas editions do not establish an Australian STP service. A Sage HR-led employer needs an identified Australian payroll connection and separate adviser permissions for that payroll file.

EasyPay also needs an exact product identity. Access EasyPay’s Singapore documentation covers Singapore payroll and CPF reporting. It is different from the historical Datacom EasyPay Australia name. Datacom’s Australian payroll page now describes Datapay. Treat those as separate candidates, with Australian reporting and handover requirements established for the actual edition before selection.

An Australian payroll file does not establish global tax compliance. Employment Hero’s partner material names Australia, New Zealand, Singapore, Malaysia and the UK. Xero’s Australian payroll, MYOB’s Australian setup and QuickBooks Australia’s payroll guidance support Australian administration. Reckon’s Australian Phase 2 material also concerns Australian reporting. For staff working overseas, identify the employment country and engage the relevant local adviser or payroll provider before treating an Australian pay run as sufficient.

Claims about tax-filing payroll software also need a country. Australian STP reports employee pay, withholding and super information. It does not lodge the employer’s income-tax return. HR and leave modules supply employee information, but PAYG payment and state payroll-tax assessment remain separate jobs.

A weekly payroll tax table usually means the ATO table for employee PAYG withholding. A state payroll-tax rate applies to an employer’s taxable wages under state rules. Use the ATO’s withholding tables for the payment period and test the payroll calculation against the applicable table. State assessments belong with payroll tax software checks.

What STP Phase 2 Requires of the Product

Single Touch Payroll (STP) sends employee pay, tax and super information to the Australian Taxation Office (ATO). Phase 2 requires more detail about the payment and the employee’s circumstances.

Inspect the income type and any required country code. Check that gross payments are separated into the correct components, including overtime, bonuses, paid leave and allowances. Salary sacrifice must have its own correct treatment. A pay item called allowance does not establish which ATO allowance category applies.

The ATO’s Phase 2 guidance distinguishes income streams, payment components and identifying fields. Compare those requirements with the product’s Australian Phase 2 documentation. Confirm that the client file has completed its required setup and that an accepted event contains the expected fields. An old product deferral does not establish permission to continue using Phase 1.

Before the first lodgement after a software change, record the old business management software (BMS) identifier and each employee’s payroll identifier. A login or software subscription ID is a different identifier. Where the destination uses previous BMS and payroll ID fields, enter the old identifiers using its documented conversion method.

MYOB’s STP setup guidance explicitly asks for the previous BMS ID where the employer has reported through another product in the same payroll year. Carrying year-to-date earnings into a new identifier without resolving the old reporting record can duplicate an employee’s income statement. Inspect the first accepted event and the employee reporting records before another pay run repeats the error.

A wrong income type can misclassify earnings even when gross pay and tax totals look correct. Trace it to the employee record and pay categories. Correct those records, submit the required correction or update event and retain its acceptance receipt. Check any affected withholding calculation separately.

Payday Super and What the Product Must Be Able to Do

Payday Super requires the payroll and payment path to support super with each payday. Under the ordinary rule, the fund must receive the contribution within seven business days, subject to specific extensions.

The ATO’s Payday Super system guidance sets out the commencement boundary and payment requirements. It states a 12% calculation on qualifying earnings. Qualifying earnings brings ordinary time earnings and other relevant payments together. Check the product’s updated earnings treatment, not an old setting that assumes every contribution uses the former quarterly process.

For each employer, identify the clearing house or gateway, its payment method and the time between approval and fund receipt. Test whether the practice can initiate contributions at each pay run and see rejected payments. A product’s super calculation does not establish that its payment service meets the receipt requirement.

A client whose product only supports quarterly batching needs a different payment arrangement or software configuration. Tell the employer exactly which step prevents timely payment and assign a person to change it. Keep the detailed employer duties with the Payday Super checklist.

Retain the payday, earnings basis, contribution amount, authorisation time, dispatch time and payment reference. Record fund receipt or rejection and the correction taken. Those records distinguish a late approval from a payment that was sent but failed downstream.

Taking Over an Employer Client’s Payroll

Take over payroll only after you have access, source records and a reconciled starting position. A pay run due soon is a reason to make the handover precise.

Obtain the employer details and payroll file access. Collect year-to-date earnings and tax, the last accepted STP event, employee records, super fund details and TFN declarations. Include leave balances, salary-sacrifice agreements and the award or agreement the employer applies. Collect sensitive employee information through a secure channel. The new employee forms guide covers starter documents.

1. Reconcile year-to-date gross components and tax to the accepted STP record. Investigate differences employee by employee before carrying them forward.
2. Match super payable with contributions sent and received. Separate unpaid liabilities from payments awaiting processing or correction.
3. Match withheld tax with the employer’s lodged activity statements and payment records. An STP receipt does not prove the ATO has been paid.
4. Confirm authority to act and the nominated reporting arrangement. Retain the client’s declaration or standing authority under the applicable ATO arrangement.
5. Review the next draft pay run against approved hours and employee changes. Obtain client approval before the agreed person lodges or releases payment.

Relationship Authorisation Manager (RAM) authorises named staff to act for a business using myID. Access Manager controls ATO permissions and the hosted-software nomination. For an agent lodgement, the practice also needs the recognised agent-client relationship. The ATO’s cloud authorisation guidance explains that the software ID and relationship are checked when a report arrives.

A mid-year software move can duplicate year-to-date reporting if the opening figures and identifiers are inconsistent. The simplest cut-over is the first pay of a new payroll year after the old year’s reporting is resolved. A mid-year boundary immediately after a completed pay run also works with a documented transfer method and reconciled year-to-date records. Never switch halfway through an unapproved run.

Put the operating split in writing. Name who supplies hours, approves employee changes, approves the run and submits STP. Separately name who releases wages, pays withheld tax and authorises super. Include the backup person and what happens when approval arrives late. Use the bookkeeping onboarding checklist for the wider engagement.

Moving a Client Onto Different Payroll Software

Move payroll through a reconciled trial before the first live submission. Employee import is only one part of the conversion.

1. Run a parallel calculation using the same approved source hours. Keep it unsubmitted and unpaid. Compare every earnings component, withholding amount, super calculation and net pay.
2. Set opening year-to-date figures using the agreed STP method. Reconcile gross components, PAYG, super and any other required reporting totals against the source file.
3. Import supported employee fields. Re-enter unsupported declarations, pay categories, permissions or fund settings from the original records.
4. Enter opening leave balances and confirm their units. Hours imported as days can produce a plausible-looking but wrong balance.
5. Obtain employer sign-off, process one live run and inspect the accepted STP event. Confirm wage payments and super status separately before repeating the process.

Record	What can transfer	What must be checked or rebuilt
Employee details	A documented employee import can carry the fields in its import specification.	Declarations, bank details and fund records need source checks.
Current-year earnings	Opening figures can carry supported year-to-date components.	The BMS method must prevent duplicate reporting.
Leave balances	Supported opening balances can carry quantities.	Units, leave categories and accrual rules need review.
Earlier pay runs	Exports preserve history outside the new product.	Do not assume an employee import recreates old payslips or STP events.

Connect the accounting product, approved timesheets and the super payment service during the trial. Map wage expense, PAYG and super liabilities to the correct accounts. Reconcile the resulting journal with the pay report before accepting the connection.

Payroll APIs transfer specified records through an authorised connection. Employment Hero publishes integration guidance for HR and timesheet connections. Identify which system supplies employee details, approved hours and leave. Give bank-detail changes a named owner and approval step. Limit the connection’s permissions to the records it needs.

A product-supplied connector handles the objects its specification lists. A custom connection is needed when the required fields or direction sit outside those limits. Test failed records and repeated imports. An import that runs twice must not create two sets of paid hours.

Rostering plans hours. Approved timesheets establish the hours paid. Compare both before payroll, including overtime and changed shifts. A manager must approve differences before the practice submits the pay run.

For an illustrative fifteen-person employer, reconcile fifteen employee records before comparing totals. One missing employee and one duplicate can leave the record count unchanged. Compare identifiers and individual balances as well as totals.

Retain the old file’s reports and source records before cancellation. The Fair Work record-keeping rules require seven years for employee records. The ATO business record guidance generally requires five years, with longer periods for some records. Use the longer applicable period and retain unresolved dispute records as required. Keep a readable backup while resolving any failed first submission.

Checks the Practice Makes Inside a Client’s Payroll File

Review each pay run against the employee records and approved source hours. A successful calculation can still use the wrong award classification or withholding declaration.

Check the award or agreement, classification, ordinary hours and overtime triggers. Review casual loading, penalties, allowances and any annualised-wage arrangement. An automated award engine applies configured rules. It cannot establish the correct instrument or classification from an employer’s unsupported assumption. Resolve a disputed classification with appropriate industrial advice.

Check super eligibility and the earnings basis, including ordinary time earnings and qualifying earnings under the applicable rules. Review leave accrual, salary sacrifice and termination payments. A salary-sacrifice deduction changes taxable pay only where the arrangement and payment type support that treatment. Reconcile the deduction with the super or benefit record and its reporting category.

Select the PAYG table for the pay frequency, employee declaration and applicable tax treatment. Review residency, tax-free-threshold and study-loan settings where relevant. Part-time or casual employment does not create its own annual income-tax scale. Compare the withheld amount with the employee’s actual pay-period earnings and the applicable ATO table.

For a bonus or irregular payment, use the ATO’s additional-payment withholding guidance. Reconcile the calculation with ordinary earnings and the period the payment covers. Do not apply a flat bonus rate without checking the prescribed method. State taxable-wages treatment is a separate assessment.

Restrict payroll access to staff who need pay rates and employee information. Confirm bank-detail changes independently through an established contact channel. Retain who requested the change, who checked it and who approved it. Reconcile HR-supplied starters, leavers and approved leave with the payroll records before the run.

Run Xero Payroll for the Employer

Give each practice staff member their own invited user and payroll permissions. Check the employer’s reporting details, employee declarations and mapped pay items. Reconcile opening balances before using them in the first run.

Xero’s Australian payroll material describes employee spreadsheet imports, opening balances, payslips and employee access through Xero Me. Review the draft run against approved hours, withholding and the earnings basis for super. Assign the STP sender explicitly and retain the submission result.

After the run, compare payslip totals with the pay report and wage payment file. Give employees access to their payslips through the agreed secure method. Reconcile super payable with payment records and fund outcomes. A visible payslip does not prove the super contribution arrived.

For a rejected STP event, read the rejection and check identifiers, declarations and mapped pay items. Repair the cause and submit using the product’s documented correction method. For an accepted but incorrect run, preserve the original records and reconcile the adjustment before sending a correction. Confirm the corrected year-to-date figures in the accepted event.

Retain employee balances, period reports, payslips and receipts at handover. The STP finalisation guide covers the separate year-end task.

If you discover an earlier underpayment, preserve the records before changing them. Establish the affected employees, hours and pay conditions. Tell the employer the calculated difference and agree the correction process, including arrears and reporting. Do not bury an old shortfall in the current ordinary-hours line.

Handing a Client’s Payroll Data Back or on

Hand payroll on with a complete record of what has been paid, reported and left outstanding. The employer’s duty to keep records continues after your engagement ends.

Supply period payroll reports and payslips, employee details and leave balances. Include STP acceptance records, the year’s finalisation status and super payment history. Identify unpaid or rejected contributions, pending corrections and the next pay run. Provide sensitive employee records through the agreed secure transfer method.

Confirm the employer can open and retain the files for the applicable record periods. Agree who holds the archive and how a former employee’s query will be answered. Keep access and retention responsibilities separate from subscription billing.

Agree the last run your practice processes and the first run the incoming bookkeeper processes. Confirm the source hours, approval contact and pending employee changes in writing. Obtain receipt of the opening figures and outstanding-items list.

After the agreed transfer, remove your named software users and unused integration permissions. Revoke the relevant ATO authority and hosted-software nomination where it is no longer needed. Avoid removing a shared nomination that still supports another authorised service. Retain evidence of the access removal and the agreed responsibility boundary.

Sector Requirements for a Client’s Payroll

Shortlist payroll by the workforce’s pay conditions and the practice’s approval duties. An industry label alone does not tell you which rules the file must apply.

Employer scenario	What the practice tests	Shortlist direction
Construction or contractor business employing staff	Site allowances, travel, approved timesheets and the employer’s identified award or agreement.	Employment Hero or QuickBooks advanced payroll where configured workforce rules fit.
Healthcare, aged care or childcare	Shift patterns, classifications, penalties and changes between employee roles.	A workforce payroll product with tested rules and separate approvals.
Hospitality, restaurants or retail	Casual loading, changing rosters, breaks and penalty hours.	Compare roster inputs and award-rule configuration before choosing.
Salon or spa	Variable hours, employee commissions and leave records.	A payroll module for simpler pay or a workforce product when rules become complex.
Manufacturing or trucking	Overtime, shift or travel allowances and approved time records.	Test actual shifts and allowance categories in the candidate product.
Recruitment agency	Multiple assignments, variable hours and approval by the right manager.	Bureau or workforce payroll with reconciled imports and employer-level access.
Consultancy employing staff	Salary changes, part-time hours and payroll approval responsibilities.	Xero, MYOB or QuickBooks where the existing accounts and payroll needs fit.

Paying a construction employee and paying an independent contractor’s invoice are different records. Consultants also need that distinction when a supplier works beside employees. Establish worker status separately before deciding which payroll records apply.

For a nonprofit employer using salary packaging, establish its eligibility and the arrangement’s tax treatment before configuring deductions or reporting. Test the package against taxable pay, super and any applicable fringe-benefit reporting. Industry membership alone does not establish a concession.

For the fifteen-person employer with a pay run due soon, keep the existing product if named access and reconciled records let your practice operate it safely. Move only when the actual reporting, payment or workforce requirement cannot be met. The next live run needs approved inputs, a recognised sender and separate evidence that each payment reached its destination.