Payroll in Malta

Managing payroll in Malta goes beyond issuing payslips. It involves employer registrations, employee onboarding and offboarding, monthly and annual tax filings, JobsPlus notifications, and accurate handling of leave and allowances. Even small errors can lead to penalties, delays, and unhappy employees. 

Payroll is where employment law, tax compliance, and social security intersect. Getting it right requires clean data, clear timelines, and a process that covers routine cycles and exceptions like corrections and allowances. 

At EMCS, we deliver a compliance-first payroll service from initial setup to year-end reporting. You’ll have: 

• A single point of contact 
• Defined cut-off dates 
• Proactive reminders for deadlines 

Employees enjoy a secure online portal for payslips and year-end forms, while you receive timely confirmations that all filings are complete. 

What is included in Our Payroll Service 

• Employer set-up - Payroll software configuration, CFR Online access, PE number activation, JobsPlus account creation. 
• Employee onboarding - NI and income tax numbers, FS4 collection, configuration in payroll, JobsPlus engagement, A1 certificate applications where applicable, introductory payroll brief, EHIC guidance. 
• Payroll processing - Monthly calculations, payslips, adjustments and corrections, secure delivery. 
• Monthly reporting - FS5 preparation and submission. 
• Annual reporting - FS3s for employees and FS7 for the employer, reconciliations, and a year-end summary. 
• Employee offboarding - Final pays, FS3 issuance, JobsPlus termination notices, basic guidance on final tax return steps. 
• Leave and attendance - Set-up and administration of leave rules and attendance records for payroll accuracy. 
• Expenses and allowances - Administration of expense reporting and allowance claim systems. 
• Timekeeping systems - Advice on, or administration of, client or EMCS-managed time capture. 

How we work 

• Clear calendar of cut-offs and deliverables 
• Rapid response to queries and corrections 
• Audit-ready logs of filings and submissions 
• Regular or ad hoc management reports