Nucleus Payroll - Payroll Made Smooth, Tax Made Simple

The Spark Behind Nucleus Payroll

Payroll is one of those things that has to be right - every single time. But as our teams grew, payroll started taking more time and more re-checking than it should. We were doing the core work in Excel, then cross-checking with attendance records, leave sheets, overtime, holiday calendars, and salary structures - again and again.

It wasn’t that Excel was “bad.” It just wasn’t built for a growing shared service team with real-life payroll complexity. So, we built Nucleus Payroll, linked with Nucleus - our core HR and project management application, so payroll could run on approved data, not on last-minute patchwork.

The Challenge: Where Payroll Used to Get Risky

Before the app, payroll processing involved a long list of manual steps:

• Manually verifying worked days/hours against attendance
• Rechecking leave, substitute leave, holiday, and overtime adjustments
• Handling joiners and leavers mid-month with proportional calculations
• Tracking increments and updating salary structures manually
• Adding allowances and one-off adjustments manually
• Managing deductions (SSF, retirement, insurance, advances, etc.) across sheets

The toughest part was always payroll tax. Nepal’s tax rules are detailed, slab-based, and tied to annual estimates - so each month required careful projection, tracking tax deducted so far, and adjusting for items like festival allowance and changing income. Doing this cleanly in Excel required constant recalculation and cross-checking.

Termination calculations added another layer: leave encashment, festival allowance accruals, final settlement, and different tax treatment- usually under time pressure.

Even the outputs were manual:

• Payslips via mail merge (risk of mismatch)
• Net pay lists prepared separately
• Bank letters typed out and rechecked with account details

It took time, and it demanded full attention.

The Solution: Meet Nucleus Payroll

Nucleus Payroll pulls approved hours/days from Nucleus and calculates payroll in one connected flow.

What It does:

• Uses approved hours/days from Nucleus (no re-entry)
• Auto-adjusts leave, substitute leave, holidays, and overtime
• Calculates salary proportionately for partial months (joiners/leavers)
• Applies each employee’s salary structures and increments correctly
• Allows additional allowances to be added during processing
• Auto-applies standard deductions (SSF, retirement, insurance, advances, etc.)
• Calculates monthly payroll tax automatically, with clear visibility of:
  • Annual estimated income
  • Taxable benefits and deductions
  • Tax deducted so far
  • Monthly tax deduction and remaining tax

• Generates and emails payslips directly from the app
• Produces the bank letter and net pay list in the required template, with bank details already in the system
• Includes a separate termination module for final settlement, encashments, and correct tax treatment (then picked up in the next payroll cycle)

It’s built to be easy to run - but also easy to review.

How We Built It

This was built from real payroll cycles - by the same people who run them. HR and Finance mapped the real checks that matter, team leads shared where approvals and exceptions usually slow things down, and IT built the flow around Nucleus, so everything stayed connected. We tested it using our own tricky cases (increments, partial months, overtime, terminations) until it handled them cleanly.

The goal was simple: fewer manual steps, clearer checks, and a process people can trust.

The Impact: Payroll That’s Easier to Run (and Easier to Review)

The biggest change wasn’t just fewer checks - it was time. Earlier, payroll processing and salary crediting typically took 7 days into the next month. With Nucleus Payroll, we’ve had cycles where payroll was processed and salaries were credited on Day 1 (the 1st of the next month).

What improved in practice:

• Much faster payroll processing with fewer repetitive checks
• Clearer tax overview month-by-month (and easier review)
• Lower risk of payslip/email mismatches
• Cleaner records for future audits and reporting
• Less stress during payroll week

And most importantly: payroll became something the team could run with confidence, not anxiety.

 Closing Statement

Payroll will always be sensitive - and it should be. People rely on it. Nucleus Payroll didn’t change that responsibility - it removed the unnecessary manual work around it. It just made the process simpler, cleaner, and easier to manage.

Like our other tools, it wasn’t built to impress. It was built to work - built for how we work, built to run every month.