HR & Payroll Software for Nigeria
The Nigeria Tax Act 2025 rewrote PAYE from 1 January 2026. If your payroll still applies the Consolidated Relief Allowance, it has been computing the wrong tax all year. We build payroll that gets it right — custom, Odoo or ERPNext.
250+
Projects Delivered Since 2020
NTA 2025
PAYE Bands Implemented
Odoo & ERPNext
Localisation Specialists
₦2.5M–₦18M
Typical Payroll Build Range
We reply on WhatsApp within minutes.
Your Payroll Is Probably Wrong Right Now
On 1 January 2026 the Nigeria Tax Act 2025 replaced the PAYE regime that every Nigerian payroll system had been built around since 2011. This was not a rate tweak. It removed a relief that sat at the centre of the calculation and replaced the whole band structure.
What changed, in the order it will break your spreadsheet:
- The Consolidated Relief Allowance was abolished. Every payroll formula that starts with "higher of 200,000 or 1% of gross, plus 20% of gross" is now computing a relief that no longer exists.
- New progressive bands of 0%, 15%, 18%, 21%, 23% and 25% replaced the old 7% to 24% ladder.
- A ₦800,000 tax-free threshold means low earners drop out of PAYE entirely — and your system needs to stop deducting from them, not deduct a small amount.
- Rent relief arrived: 20% of annual rent paid, capped at ₦500,000. That means capturing and evidencing rent per employee, which no legacy Nigerian payroll field exists for.
- NHF became voluntary. Your system now needs a per-employee opt-in flag, an audit trail for it, and the ability to stop mid-year.
- TIN is mandatory, so employee records need validation at onboarding rather than at year end.
The practical consequence. If nobody re-engineered your payroll in January, you have been under- or over-deducting PAYE for the whole of 2026, your monthly remittances to the state internal revenue service do not reconcile, and your year-end reconciliation is going to be painful. This is the forced re-tooling event, and it is the reason this page exists.
Build, Localise or Subscribe — An Honest Comparison
We will not pretend a custom build is right for everyone. There are three sensible routes and the right one depends mostly on your headcount and how unusual your pay rules are.
| Route | Best for | Rough cost | The catch |
|---|---|---|---|
| Nigerian payroll SaaS (SeamlessHR, PaidHR, Bento and similar) |
Standard employment, 20–500 staff, no unusual allowances | Commonly ₦2,000–₦20,000 per employee per month depending on tier and vendor | Per-seat pricing compounds as you grow, you bend your process to their model, and your data lives in their system. Genuinely the right answer for many businesses — we will tell you when it is. |
| Odoo or ERPNext localisation | Businesses already on an ERP, or wanting payroll joined to accounting and inventory | ₦2,500,000–₦8,000,000 one-off plus support | You need someone who can write the Nigerian salary rules properly. Out-of-the-box Odoo and ERPNext payroll are not Nigerian and never will be. |
| Custom build | Unusual pay structures, multi-entity groups, outsourcing and payroll bureaus, 500+ staff | ₦6,000,000–₦18,000,000 | Longer to first payroll run, and you own the maintenance. Pays for itself when per-seat SaaS at your headcount costs more annually than the build did once. |
A worked example, because the crossover point surprises people. At 400 staff and ₦6,000 per employee per month, SaaS costs ₦28.8 million a year, every year. A ₦10 million custom build with ₦3 million annual support pays for itself inside six months and keeps paying. At 40 staff the same arithmetic says buy the SaaS. Tell us your headcount and we will do this sum honestly, even when it ends with us not selling you a build.
What the Payroll Engine Has to Get Right
PAYE under the new bands
Gross to taxable income under NTA 2025 rules: statutory deductions, pension, the rent relief calculation with its ₦500,000 cap, the ₦800,000 threshold, then the 0/15/18/21/23/25 ladder applied progressively. Annualised and spread monthly so a December bonus does not wreck the December payslip. Prior-period adjustments recompute cleanly instead of being bolted on.
Pension and PenCom
8% employee and 10% employer on basic, housing and transport, with voluntary contributions handled separately, correct treatment for staff below the mandatory threshold, and a schedule per PFA in the format your PFAs accept. Remittance reference tracking so you can prove a contribution landed.
NHF, NSITF and ITF
NHF as a per-employee opt-in with the consent record attached, since it is now voluntary. NSITF at 1% of payroll and ITF at 1% of annual payroll for employers in scope, calculated and scheduled rather than remembered in a panic each year.
Multi-state SIRS filing
Staff in Lagos, Abuja, Rivers and Delta mean four different internal revenue services, four schedules and four remittance deadlines. The system splits by employee tax jurisdiction automatically and produces each schedule in its own format instead of one file you then hand-edit four times.
Bank payment files
Net pay exports in the formats Nigerian banks actually ingest for bulk salary upload, plus direct integration through Paystack or Flutterwave transfers where you would rather push payments from the system and have them reconcile themselves.
The HR half
Employee records and documents, leave with Nigerian public holidays preloaded, attendance and shift rosters, loans and salary advances amortised against payroll, appraisals, onboarding and exit checklists, and a self-service portal where staff pull their own payslips instead of emailing HR.
Payroll Bureaus and Outsourcing Firms
If payroll is your product rather than your overhead, the requirements change completely and most SaaS does not serve you well. We build multi-tenant bureau platforms: one login, many client companies, each with its own pay calendar, tax jurisdictions, approval chain and branding on the payslip.
That means client-level segregation of data, a consolidated view for your operations team, per-client billing tied to processed headcount, bulk approval workflows so one reviewer can clear fifteen payrolls in a morning, and an audit trail that survives a client disputing a figure from eight months ago.
One warning worth stating plainly: a payroll bureau processes personal and financial data for thousands of people, which almost always makes you a data processor of major importance under the Nigeria Data Protection Act. You will need NDPC registration and an annual compliance audit. We cover what that involves on our NDPA compliance audit and CAR filing page, and we build the consent, retention and access-log plumbing into the payroll platform itself rather than leaving it as a policy document.
Migration: The Part That Actually Goes Wrong
Nobody fails at payroll software because the tax formula was hard. They fail at migration. Here is how we do it.
Parallel running, always
We run the new system alongside your existing process for two full pay cycles. Every employee's net pay is compared line by line. We do not switch you over until two consecutive months reconcile to the naira.
Year-to-date carry-in
Mid-year migration means importing YTD gross, YTD PAYE, YTD pension and YTD NHF per employee, or the annualised tax calculation for the rest of the year will be wrong and every payslip after go-live will be too.
Data cleanup first
Duplicate employee records, missing TINs, wrong PFA codes, staff who left in 2023 still on the register. We clean before we import, because importing dirt just relocates it.
Train the person who runs it
Two sessions with your payroll officer, a written runbook for the monthly cycle, and we sit with them through the first live run. Software nobody can operate is not a solution.
Cost and Timeline
NTA 2025 remediation
from ₦1,200,000
You already have a payroll system, it is just wrong since January. We rewrite the tax engine, add rent relief and the NHF opt-in, recompute the year to date, and produce the reconciliation your auditor will ask for. Three to five weeks.
Odoo / ERPNext payroll
₦2,500,000 – ₦8,000,000
Nigerian salary rules, PAYE, pension, NHF, NSITF and ITF written as proper localisation on top of your ERP, joined to the general ledger so payroll journals post themselves. Eight to fourteen weeks.
Custom HR & payroll
₦6,000,000 – ₦18,000,000
Full platform: payroll engine, HR module, self-service portal, multi-state filing, bank integration and reporting. Bureau and multi-entity builds sit at the top of the range. Four to seven months.
Support afterwards runs from ₦150,000 a month and includes keeping the tax engine correct as rules change — which, on the evidence of January 2026, is not a theoretical benefit.
Related Musskart Pages
Already running an ERP?
If payroll is one piece of a wider finance and operations problem, start from ERP software development in Nigeria — that page covers the full Odoo and ERPNext picture, and payroll drops into it as a module rather than a separate system to reconcile.
- FIRS / NRS e-Invoicing Integration — the other half of your 2026 tax compliance work
- Accounting & Invoicing Software for Nigeria — bookkeeping, VAT and WHT for SMEs
- NDPA Compliance Audit & CAR Filing — payroll data makes you a processor of major importance
- Custom Software Development Cost in Nigeria — how we scope and price a build
- Musskart Pricing — how we price work across all our services
- Contact Musskart — phone, email and office details
Frequently Asked Questions
Get Your Payroll Correct Under NTA 2025
Send us your headcount, how you run payroll today and whether anyone touched the tax rules in January. We will tell you honestly whether you need a fix, a localisation or a build — and what each would cost.
