AutoCount Cloud HRMS Setup Guide: Payroll, EPF, SOCSO and PCB in Malaysia

AutoCount HRMS Setup: What You Need to Know First

Setting up AutoCount HRMS for Malaysian payroll comes down to four stages: configure the company, load employees with the correct statutory details, define pay items, and run a parallel payroll before going live. If those stages are done in order, AutoCount Cloud HRMS calculates EPF, SOCSO, EIS and PCB automatically and produces the files and forms you need for KWSP, PERKESO and LHDN.

This guide walks through each stage using the menu names from AutoCount’s own documentation, and flags the 2025 to 2026 statutory changes that affect setup. It is based on how iDynamics configures AutoCount Cloud HRMS for SMEs, so it also covers the mistakes we most often fix after a self-setup.

Before You Start: Information to Collect

Gather these items before you log in. Missing details are the most common reason a first payroll run is delayed.

Step 1: Configure the Company in AutoCount HRMS

1. Create the subscription and company: new users create a subscription and company in the AutoCount subscription portal. One subscription can hold multiple companies, each with its own access rights.
2. Complete the company profile: enter employer statutory numbers, address and company logo for payslips and reports.
3. Set the calendar: confirm public holidays for your state, add any extra company holidays, and set rest days, including half-day or alternate Saturdays if you use them.
4. Define departments and approvals: choose approval by organisation chart or by department, and decide between flat and sequential approval for leave, claims and overtime.
5. Invite payroll users: give HR and finance users the right access level, and restrict who can view which groups of employees.

Take time on approvals. A clear approver and backup for every department is what makes eLeave and eClaim work on the AC Payroll mobile app.

Step 2: Add Employees and Statutory Settings

For more than a handful of staff, use the Excel import for employee information rather than keying records one by one. Then open each employee under Payroll, Employee Maintenance and check the Statutory Requirement tab.

EPF

Under the KWSP Third Schedule, Malaysian employees below 60 contribute 11%, with the employer contributing 13% for wages of RM5,000 and below and 12% above RM5,000. For employees aged 60 and above, the employer rate is 4% and the employee rate is 0%. Non-Malaysian employees with a valid passport and work pass contribute 2% each from October 2025 wages, as stated on the KWSP employer contribution page. Contributions follow wage bands in the schedule rather than exact percentages for most salaries, which the system handles automatically.

SOCSO, EIS and LINDUNG 24 Jam

• SOCSO first category (employees under 60): employer 1.75% and employee 0.5% of monthly wages.
• SOCSO second category (60 and above): employer 1.25%, Employment Injury Scheme only.
• EIS: 0.2% employer and 0.2% employee, for employees aged 18 to 60.
• LINDUNG 24 Jam: from 1 June 2026, an employee-borne contribution of 0.75% for non-work accident cover.

SOCSO, EIS and LINDUNG 24 Jam contributions are capped at a wage ceiling of RM6,000. See the PERKESO contributions page for the current tables.

PCB and HRDF

Set the number of children and relief points that apply, spouse status, and any contributions borne by the employer, because these change the PCB amount. If you are registered with HRD Corp, tick HRDF contribution for eligible employees and set the HRDF rate at company level: HRD Corp applies 1% for employers with 10 or more Malaysian employees and 0.5% for the optional 5 to 9 employee category.

Step 3: Set Up Pay Items, Overtime and Leave

Pay items are where most payroll errors start, because each item carries its own statutory treatment. Build the list from your last three months of payslips so nothing is missed, including one-off items such as arrears or incentive payments.

• Recurring allowances: create monthly recurring allowances, and set whether each one is subject to EPF, SOCSO, EIS and tax.
• Commission and bonus: AutoCount lets you set whether commission, bonus and similar items contribute to EPF, SOCSO and tax. Get this right before the first bonus month.
• Overtime and lateness: define default overtime formulas, rounding rules and lateness deductions. If you use eAttendance, set shift and rule maintenance, including GPS, Wi-Fi, Bluetooth or facial recognition clocking.
• Benefits in kind: set up BIK such as company cars using LHDN prescribed values, so they appear correctly on the EA form.
• Leave and claims: enable eLeave and eClaim, set entitlements, carry forward rules and claim limits, and match maternity and paternity leave to your current policy.

Step 4: Load Year-to-Date Figures and Run a Parallel Payroll

If you go live after January, upload year-to-date payroll transactions or previous employment entries. PCB is cumulative across the year, so skipping this step produces wrong PCB for the rest of the year and an EA form that does not match your old records.

1. Create a payroll process for the month and select the employees.
2. Use Save and Recalculate All after any changes to pay items or employee settings.
3. Compare gross pay, EPF, SOCSO, EIS, PCB and net pay for every employee against your current payroll.
4. Investigate differences of even one ringgit. They usually point to a pay item flag, an age category or a missing relief.
5. Repeat for a second month if the first run had many differences.

Once the parallel run reconciles, go live and invite employees to the Employee Self Service portal and AC Payroll app so they receive payslips and submit leave and claims there.

Connect payroll to your accounts

Before the first live month, agree how payroll should post to your general ledger: salary expense by department, employer EPF, SOCSO and EIS expense, and the liabilities for amounts payable to KWSP, PERKESO and LHDN. AutoCount lets you define which payroll data is posted, so finance receives one journal per run instead of re-keying totals.

Step 5: Monthly Submissions and Year-End Process

Every month

• Generate the bank payment file for salaries. AutoCount publishes a list of supported bank formats.
• Download the EPF file and the SOCSO and EIS text file, and submit through the KWSP and PERKESO portals.
• Remit PCB through LHDN’s e-PCB, e-Data PCB or e-CP39 channels, then record PCB and CP38 receipt details in the system.
• Pay EPF, SOCSO, EIS, PCB and the HRDF levy by the 15th of the following month.
• Post payroll to AutoCount Cloud Accounting, or to AutoCount Accounting on desktop through the payroll posting plug-in.

New joiners and leavers

LHDN requires CP22 within 30 days of a new employee starting and CP22A at least 30 days before a private sector employee’s cessation, both now submitted through the MyTax portal. Set resign dates in the system so final payroll and the EA form are correct.

Year end

Run the Year End Process, use the EA Assistant to check mappings, and generate EA forms. Employees must receive their EA form by the last day of February, and employees can download it themselves through ESS. Export the CP8D text file and submit Form E by 31 March through e-Filing.

Common AutoCount HRMS Setup Mistakes

These are the issues iDynamics most often corrects when a company has set up AutoCount HRMS on its own. Each one is easy to prevent at setup and slow to fix later.

• Old EPF settings for foreign staff: non-Malaysian employees left without EPF after the October 2025 change, which creates arrears and late payment charges once discovered.
• Missing LINDUNG 24 Jam deduction: payroll not updated for the employee contribution from June 2026, so PERKESO amounts do not match what is due.
• One generic allowance: items with different EPF, SOCSO or tax treatment grouped together, so contributions and PCB are wrong every month.
• No year-to-date figures: going live mid-year without previous earnings, which breaks cumulative PCB and the EA form.
• Age changes ignored: employees turning 60 kept on first category SOCSO and standard EPF rates instead of the age-based rates.
• No backup approver: leave and claims stall when a manager is on leave, and staff go back to WhatsApp approvals.

A short review after the first three payroll cycles catches most of these before they reach year end.

Next Steps: Get Your AutoCount HRMS Set Up Right

A careful setup takes longer up front but saves months of corrections. If you prefer a guided implementation, iDynamics handles data migration, statutory configuration, accounting posting and parallel runs for AutoCount Cloud HRMS, and we run HRDF claimable AutoCount training for your HR team.

Talk to an iDynamics consultant for a free review of your payroll setup or a demo of AutoCount Cloud HRMS with your own pay items.

Frequently Asked Questions