Run Monthly Payroll

This article walks you through a monthly payroll in IntBooks: open a period, compute payslips, submit the run, then export the bank and statutory files. IntBooks prepares the files; you upload them to your bank and to the KWSP, PERKESO and LHDN portals, which do the actual remittance.

Beta note. IntBooks is in closed beta. The payroll module does not yet apply three recent rules automatically: the EPF rates for employees aged 60 and above, EPF for non-citizen employees (mandatory from October 2025 wages), and PERKESO’s LINDUNG 24 Jam deduction (from the June 2026 contribution month). Adjust those employees by hand until this note is removed. The rules are summarised in Step 4.

Prerequisites

• The HR & Payroll module is enabled for your organisation
• All employees have active employment records under HR → Employees
• Each employee has a bank account number for salary disbursement
• Each employee has an NRIC or passport number and tax number for statutory files
• A salary structure is assigned to each employee (basic + allowances + deductions) under HR → Payroll → Structures

Step 1: Open a payroll period

Go to HR → Payroll → Periods and make sure the month you want to pay is open. A payroll run can only be created for an open period.

Step 2: Create the run

Go to HR → Payroll → Runs → New Payroll Run, select the open period, give the run a name (for example, September 2026 Payroll) and click Create Run.

Step 3: Compute payslips

Open the run and click Compute Payslips. For each employee, IntBooks works out:

• Gross pay from the employee’s salary structure (basic, fixed allowances, variable pay)
• Worked days, taking account of attendance and approved leave where the Time & Attendance and Leave modules are in use
• Statutory deductions (Step 4)
• Net pay

Review the payslips on the run’s review screen. If a value is wrong, fix the underlying record and compute again.

Step 4: Check the statutory deductions

IntBooks calculates EPF, SOCSO, EIS, the HRD Corp levy and PCB. The current rules, for reference:

EPF (KWSP)

Employee	Employer	Employee share
Citizen or PR under 60, wages RM5,000 or less	13%	11%
Citizen or PR under 60, wages above RM5,000	12%	11%
Aged 60 and above	Minimum 4%	0%
Non-citizen employee (from October 2025 wages)	2%	2%

Sources: KWSP, KWSP on employees above 60, KWSP on non-citizen employees. The last two rows are the ones to check by hand during the beta.

SOCSO and LINDUNG 24 Jam (PERKESO)

SOCSO follows PERKESO’s wage-band table, capped at a monthly wage of RM6,000 (since 1 October 2024). Category 1 (under 60) is 1.75% employer / 0.5% employee; Category 2 (60 and above) is 1.25%, paid by the employer (PERKESO).

From the June 2026 contribution month, LINDUNG 24 Jam adds a 0.75% employee-only deduction, up to the RM6,000 ceiling, for all employees covered by SOCSO, with no age limit (PERKESO FAQ). Add it by hand during the beta.

EIS

0.2% employer + 0.2% employee for employees aged 18 to 60, capped at RM11.90 each at the RM6,000 ceiling (PERKESO Act 800 table).

HRD Corp levy

Compulsory for employers with 10 or more Malaysian employees (1% of monthly wages); optional for 5 to 9 (0.5%) (HRD Corp FAQ).

PCB (Monthly Tax Deduction)

PCB is calculated with LHDN’s computerised calculation method from the employee’s wages, year-to-date figures, marital status, children and approved reliefs.

Step 5: Submit and lock the run

When the totals look right, click Submit & Lock. Submission is final: a submitted run can’t be edited. If you find a mistake afterwards, use Reverse on the run and create a corrected one.

Submitting the run posts the payroll journal to your general ledger automatically:

• Salary expense and employer EPF / SOCSO / EIS expense — debit
• Salary payable (net pay) — credit
• EPF, SOCSO, EIS and PCB payable — credit

You clear each payable when you pay the employees and remit to each agency.

Step 6: Download payslips

Each employee’s payslip can be downloaded as a PDF from the run. Employees can also see their payslips in the Employee Self-Service portal.

Step 7: Export the statutory files

Go to HR → Compliance & Exports. IntBooks produces:

Agency	File	Upload to
KWSP (EPF)	i-Akaun text file	KWSP employer portal
PERKESO (SOCSO)	ASSIST upload file	PERKESO ASSIST portal
PERKESO (EIS)	EIS upload file	PERKESO ASSIST portal
LHDN (PCB)	CP39 text file	LHDN’s online MTD channel

All four are due by the 15th of the following month. The HRD Corp levy file is not available yet; take the levy figure from the run and pay it on the HRD Corp portal.

Step 8: Pay the employees

Go to HR → Payroll → Bank Files, select the submitted run and a bank format, and click Generate File:

Format	Use for
Maybank	Maybank business bulk payment
CIMB	CIMB business bulk payment
RHB	RHB business bulk payment
Generic CSV	Other banks — map the columns in your bank’s upload template

Upload the file to your bank’s bulk payment screen and authorise it there. Check the first file against your bank’s current upload specification before you rely on it; if your bank rejects it, tell us at hello@intbooks.my.

Year-end

Generate Form EA for each employee from HR → Compliance & Exports. LHDN requires you to give every employee their Form EA by the last day of February, and to file Form E by 31 March (LHDN).

What’s next?

• Reconcile bank statements — match the salary payment to your imported bank statement
• Invite team members — give your HR officer access to the payroll module