User guide

PayTrove user guide

Nigerian payroll and statutory compliance, step by step

15 chapters · 126 steps with screenshots · 22 questions answered · updated 27 September 2026

This guide shows how to run Nigerian payroll in PayTrove: setting up the company and its people, running and approving monthly payroll, paying staff, remitting PAYE, pension, NHF, NSITF and ITF, handling leave, loans, casual workers, bonuses and leavers, giving employees self-service, and filing the annual returns.

It follows one fictional company, Savannah Harvest Agro-Allied Limited, through its first three months on PayTrove (January to March 2026). Every screenshot was taken from PayTrove running that scenario, so the figures in the text match the screens.

The illustration: Savannah Harvest Agro-Allied Limited

An agro-exporter (RC 1847263) that buys cashew, sesame, ginger, cocoa, shea nuts and hibiscus from farmers across Nigeria, processes them at its Kaduna factory and exports them to Europe, Asia and the Middle East. Head office: 14 Adeola Odeku Street, Victoria Island, Lagos. Year end 31 December.

LocationStaffPeoplePAYE goes to (state of residence)
Lagos head officeManaging Director, finance, payroll and HR, export sales, logistics, driver8Lagos (7), Ogun (1)
Kaduna processing factoryFactory manager, quality control, production supervisors, machine operators, maintenance, stores, and four daily-rated casual workers at ₦8,500 a day14Kaduna
Buying centresBuying officers at Lokoja, Ogbomoso, Lafia, Dutse, Kachia, Akure, Minna, Ilorin and Kano; field agents at Lafia, Ogbomoso and Dutse12Kogi, Oyo, Nasarawa, Jigawa, Kaduna, Ondo, Niger, Kwara, Kano
Total, January 20263411 State Internal Revenue Services

Monthly salaries range from ₦150,000 (field agents and machine operators) to ₦3,500,000 (the Managing Director); the four casual workers are paid ₦8,500 a day for the days they work. Factory staff receive a shift allowance and buying-centre staff a field allowance. Two employees contribute to NHF; five have declared rent for rent relief; the driver's pay is agreed as a take-home amount.

PersonJobPayTrove role
Chukwudi OkekeFinance Manager, LagosAdmin — first administrator (opens PayTrove from troveuniverse.com); approves payroll
Aisha BelloManaging Director, LagosAdmin — second approver; holds the TroveUniverse account
Blessing EtimPayroll & HR Officer, LagosPreparer — maintains employees, prepares runs, approves leave
Funmilayo AdeyemiAccountant, LagosViewer — reports, journals, schedules
Ibrahim DanjumaFactory Manager, KadunaViewer (from March)
Grace Ojo, Musa Lawal, Tobi AkinolaBuying officers (Akure, Lafia); export salesEmployee self-service
Nkechi OkaforOkafor Bello & Co, external accountantsViewer at Savannah Harvest; Preparer at two other clients (practice mode)
DateWhat happensGross pay (₦)
5–6 JanuaryPayTrove opened from troveuniverse.com; settings, users, pay components; 34 employees added; leave policy, a staff loan and a co-operative deduction set up
28 JanuaryJanuary payroll paid (prepared 26th, approved 27th)16,192,357
5–9 FebruaryJanuary pension, PAYE (eleven states), NHF and NSITF remitted
10–12 FebruarySelf-service logins; leave requested and approved; unpaid leave; a promotion and a new joiner; overtime; a salary advance; a forgotten password
27 FebruaryFebruary payroll paid16,566,928
2 MarchFebruary remittances; a fifth admin seat needed — two seats bought on troveuniverse.com
13 MarchEmmanuel Adaji leaves; final settlement paid55,385
27 MarchMarch payroll paid, with an export bonus and back pay17,298,647
31 MarchQ1 production bonus paid in its own run; quarter-end reports, annual return schedules, audit log; practice mode and client billing240,000

Who should read what

Every step says who normally does it. Start with chapter 1 (everyone), then read the chapters for your role:

Contents

  1. 1. Getting started

    Open PayTrove from troveuniverse.com, set up two-factor authentication, sign in, reset a forgotten password and find your way round the Overview.

    10 steps
    1. 1.1 Open PayTrove from troveuniverse.com
    2. 1.2 Link your authenticator app
    3. 1.3 Save your recovery codes
    4. 1.4 Sign in with your email and password
    5. 1.5 Enter the code from your app
    6. 1.6 Forgotten your password? Ask for a link
    7. 1.7 Open the email
    8. 1.8 Choose a new password
    9. 1.9 The Overview page
    10. 1.10 The latest payroll run on the Overview
  2. 2. Setting up the company

    Record the company's details, salary structure, statutory registration numbers and pension rates, and check which statutory rules apply.

    5 steps
    1. 2.1 Record the company profile
    2. 2.2 Set the salary structure
    3. 2.3 Enter the statutory registration numbers
    4. 2.4 Pension rates and record keeping, then save
    5. 2.5 Check which statutory rules apply
  3. 3. Users, roles and security

    Add staff and self-service logins with the right roles, and manage two-factor authentication and passwords.

    7 steps
    1. 3.1 Add a staff login
    2. 3.2 The users list and the four roles
    3. 3.3 Change a login's role, reset its password or remove it
    4. 3.4 Give an employee self-service access
    5. 3.5 Reset someone's two-factor
    6. 3.6 Your own two-factor page
    7. 3.7 Change your own password
  4. 4. Pay components

    Set up the allowances, bonuses and deductions that are paid on top of each employee's monthly gross.

    2 steps
    1. 4.1 Create a pay component
    2. 4.2 The company's components
  5. 5. Employees

    Add employees one by one or from a spreadsheet — salaried, take-home and daily-rated casual workers — with everything needed to pay and file for them.

    9 steps
    1. 5.1 Add an employee: person and employment
    2. 5.2 Pay and statutory details
    3. 5.3 Health insurance and bank account, then save
    4. 5.4 Pay agreed as take-home (net)
    5. 5.5 A daily-rated casual worker
    6. 5.6 Import many employees from a spreadsheet
    7. 5.7 Check the employee list before the first run
    8. 5.8 Add allowances and deductions to an employee
    9. 5.9 Keep evidence on the employee's file
  6. 6. Running the January payroll

    Prepare, check and approve the January payroll, enter casual workers' days, and produce payslips, the bank file, the register and the journal.

    15 steps
    1. 6.1 Create the run
    2. 6.2 Read the checks on the draft
    3. 6.3 Enter the days worked by casual workers
    4. 6.4 The draft picks up corrected records
    5. 6.5 Write the approval memo
    6. 6.6 Review the totals
    7. 6.7 How PAYE was worked out: a worked example
    8. 6.8 Approve the run
    9. 6.9 The line items
    10. 6.10 Casual workers on the run
    11. 6.11 A casual worker's payslip, and how their PAYE is worked out
    12. 6.12 Payslips as PDF files
    13. 6.13 The bank payment file
    14. 6.14 The payroll register
    15. 6.15 The journal for your ledger
  7. 7. Remittances

    Pay over PAYE to each state IRS, pension, NHF, NSITF and ITF from the schedules, and record every payment with its receipt.

    8 steps
    1. 7.1 The remittance ledger after approval
    2. 7.2 The PAYE schedule by state
    3. 7.3 The pension schedule for PCRS
    4. 7.4 The NHF schedule
    5. 7.5 The employer levies: NSITF and ITF
    6. 7.6 Record a remittance
    7. 7.7 The ledger after paying
    8. 7.8 Overdue remittances
  8. 8. Leave, loans and third-party deductions

    Set the leave policy, approve and book leave, and handle staff loans, salary advances and court or co-operative deductions.

    9 steps
    1. 8.1 Set the leave policy
    2. 8.2 Leave types and public holidays
    3. 8.3 Approve a leave request
    4. 8.4 Book leave for an employee
    5. 8.5 Leave balances
    6. 8.6 Adjust a leave balance
    7. 8.7 Give a staff loan or salary advance
    8. 8.8 Add a court, tax or co-operative deduction
    9. 8.9 Orders and the remittance schedule
  9. 9. February: changes to pay

    Record a promotion, overtime, a new joiner and unpaid leave, import casual workers' days, and check what changed before approving.

    8 steps
    1. 9.1 Record a promotion or pay rise
    2. 9.2 Pay one-off overtime
    3. 9.3 Import the month's days from a spreadsheet
    4. 9.4 Import the days
    5. 9.5 The February draft
    6. 9.6 What changed since January
    7. 9.7 A new joiner, prorated
    8. 9.8 Unpaid leave and overtime on a payslip
  10. 10. March: a leaver and back pay

    Pay a leaver's final settlement with pro-rata leave, then run March with back pay and a bonus.

    7 steps
    1. 10.1 Start the final settlement
    2. 10.2 Work out the settlement
    3. 10.3 Approve the settlement run
    4. 10.4 Mark the leaver inactive
    5. 10.5 The March payroll and its checks
    6. 10.6 Pay back pay (arrears)
    7. 10.7 Back pay on the payslip
  11. 11. Bonus and 13th-month runs

    Pay a bonus or a 13th month in its own run, with PAYE worked out correctly on the whole year, and correct a run approved with a mistake.

    6 steps
    1. 11.1 Create a bonus run
    2. 11.2 Check the PAYE on the bonus run
    3. 11.3 The bonus payslip
    4. 11.4 Reverse a run approved with a mistake
    5. 11.5 The reversed run, then the corrected one
    6. 11.6 All runs so far
  12. 12. Employee self-service

    What employees see on self-service: payslips, leave requests and their own contact details.

    3 steps
    1. 12.1 My payslips
    2. 12.2 Request leave
    3. 12.3 Update my contact details
  13. 13. Reports, annual returns and the audit log

    The variance, department and cost-to-employ reports, the annual returns for each state, the audit log and the PAYE calculator.

    13 steps
    1. 13.1 Cost by department
    2. 13.2 Cost to employ
    3. 13.3 The Overview at the end of the quarter
    4. 13.4 Annual returns
    5. 13.5 A state's schedule
    6. 13.6 Casual workers on the annual return
    7. 13.7 The exported employer summary
    8. 13.8 An exported state schedule
    9. 13.9 The audit log
    10. 13.10 Filter the audit log
    11. 13.11 The PAYE calculator
    12. 13.12 The calculator's workings
    13. 13.13 Work out the gross for an agreed take-home
  14. 14. Practice mode, AI assistance and offline working

    Run payroll for several client companies, bill them, set up AI assistance with your own provider, and work offline.

    22 steps
    1. 14.1 Sign in to several companies
    2. 14.2 Switch between companies
    3. 14.3 The practice view
    4. 14.4 Prepare runs for several companies
    5. 14.5 The drafts are ready
    6. 14.6 Bill your clients
    7. 14.7 Raise the month's invoices
    8. 14.8 Issue an invoice
    9. 14.9 The invoice PDF
    10. 14.10 Set up AI assistance
    11. 14.11 Acknowledge, switch on and test
    12. 14.12 Azure OpenAI settings
    13. 14.13 What AI assistance does
    14. 14.14 The AI usage log
    15. 14.15 The prompt library
    16. 14.16 Make your data available offline
    17. 14.17 The Offline page
    18. 14.18 Working without a connection
    19. 14.19 Changes made offline wait to be sent
    20. 14.20 When an offline change clashes
    21. 14.21 The company's offline policy
    22. 14.22 Where to find the offline policy
  15. 15. Your TroveUniverse subscription

    How PayTrove is billed — prepaid admin seats and monthly-counted active employees, monthly or yearly — and where to manage it.

    2 steps
    1. 15.1 When all your admin seats are in use
    2. 15.2 After buying more seats

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