Zoho Payroll setup and management services.
Regikart configures Zoho Payroll end-to-end - statutory components, salary structures, employee master, Zoho Books integration and Form 16 generation - then runs your first 2 pay cycles alongside your team. CA + CS supervised. Setup starts at Rs 9,999. Go-live in 7 to 14 working days for standard scopes.
Reviewed by Regikart CA & CS Team · 250+ clients served · 3 offices (Kolkata, Delhi, Bengaluru)
Reviewed by CA & CS Team · Regikart · Verified for EPF & MP Act 1952, ESI Act 1948, Income Tax Act 2025 Section 392 · Last updated 26 May 2026
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Leave your name and number. Our team calls you, checks your headcount and what applies to you, and sends a fixed written quote before you pay anything.
- Registrations, monthly challans and returns on the EPFO, ESIC and state portals handled by our team
- 250+ clients served from Kolkata, Delhi and Bengaluru, and remotely across India
Zoho Payroll - in one box.
Zoho Payroll is cloud-based payroll software built for Indian statutory compliance - PF, ESI, Professional Tax and TDS under Section 392 of the Income Tax Act, 2025. Regikart configures the platform, runs your first 2 pay cycles, and trains your team.
Setup starts at Rs 9,999. The Free plan supports up to 10 employees at zero subscription cost; Standard adds 25 employees at Rs 1,000/month (annual billing).
| Parameter | Detail |
|---|---|
| Governing Acts | EPF and MP Act 1952; ESI Act 1948; State PT Acts; Income Tax Act 2025 Section 392 |
| Applicable to | Any Indian business running monthly payroll (Pvt Ltd, LLP, Partnership, Proprietorship, Section 8) |
| Setup timeline | 7 to 14 working days (standard); 21+ days (multi-state, 200+ employees) |
| Setup cost | Rs 9,999 onwards (Regikart implementation), exclusive of Zoho subscription |
| Zoho subscription | Free up to 10 employees; Rs 1,000/month annual (25 employees); Rs 40 per additional employee |
| Penalty for non-compliance | EPF damages up to 100%; ESI interest 12% p.a.; TDS interest 1.5% per month under Section 201(1A) |
| Authority | EPFO, ESIC, State Labour Department, Income Tax Department (TRACES) |
Indian statutory compliance, on a single cloud platform.
Zoho Payroll is cloud-based payroll software developed by Zoho Corporation that automates salary calculation, statutory deductions and payslip generation for Indian businesses under the EPF and Miscellaneous Provisions Act, 1952, the ESI Act, 1948, applicable State Professional Tax Acts and Section 392 of the Income Tax Act, 2025.
It runs monthly pay cycles, computes employee and employer contributions for Provident Fund, Employees' State Insurance, Professional Tax and Labour Welfare Fund, generates digitally signed payslips and Form 16 Part B, and posts payroll journal entries to Zoho Books automatically.
The Free plan supports up to 10 employees; the Standard plan covers 25 employees at Rs 1,000 per month (billed annually), with each additional employee at Rs 40 per month. Regikart fees for implementation are charged separately and start at Rs 9,999.
Key terms you need to know
EPF
EPF wage ceiling: ₹25,000 a month from 17 September 2026 (it was ₹15,000 until then). Contributions for wage months from that date follow the new ceiling.
ESI
Employees' State Insurance - 0.75% employee + 3.25% employer of Gross Pay; applicable only to employees earning up to Rs 21,000 per month.
PT
Professional Tax - state-levied tax on salary; rates and slabs vary by state (Maharashtra, Karnataka, West Bengal and 16+ states).
TDS u/s 392
Tax Deducted at Source on salary income under the Income Tax Act 2025; computed monthly based on the employee's annual projected income and regime choice.
LWF
Labour Welfare Fund - small contribution by employer and employee in 16+ Indian states; usually deducted half-yearly or annually.
ECR
Electronic Challan cum Return - the monthly file uploaded to the EPFO Unified Portal that contains UAN-wise wage and contribution data.
Six entity types where Zoho Payroll earns its keep.
Any Indian business with employees on its rolls must comply with payroll statutory requirements - irrespective of whether payroll runs on paper, spreadsheets or software.
| Business type | Why Zoho Payroll setup is the next move |
|---|---|
| Private Limited Companies (1-5,000+ employees) | Automated PF/ESI/TDS compliance and audit-ready records from day one of incorporation |
| LLPs and Partnership firms | Salaried partners and employees both processed; statutory contributions on partners' salary handled |
| Proprietorships (5-10+ employees) | Excel-based payroll breaks once headcount scales; Zoho Payroll restores control |
| Section 8 Companies and NGOs | Auditable payroll records required for FCRA, CSR and grant reporting |
| Startups on Zoho Books already | Auto-posted salary journals eliminate finance + HR re-keying |
| Mid-size businesses (multi-state) | State-wise PT and LWF handling baked in; ESI sub-codes per state mapped during setup |
- EPF: mandatory once you employ 20 or more persons (voluntary below).
- ESI: mandatory once you employ 10 or more in covered states (some states 20).
- Professional Tax: mandatory in PT-levying states from the first employee.
- TDS on salary: mandatory when any employee's projected annual income crosses the basic exemption limit under the chosen regime.
Six services, one CA-led implementation.
1. End-to-End Implementation
- Organisation setup, tax information (PAN, TAN, AO code) and pay schedule.
- Statutory components (EPF, ESI, PT, LWF) configured and tested.
- Salary structure design and employee master upload.
2. Statutory Configuration
- EPF establishment code and ESI sub-code verified against existing registrations.
- State-wise Professional Tax registration mapping and LWF state matrix.
- ECR / challan workflow set up and dry-run before live filing.
3. Zoho Books and Zoho People Integration
- Auto-posting of salary expense, statutory liability and net pay journals to Zoho Books.
- Two-way sync of employee master, leave and LOP data with Zoho People.
- Account mapping done once during setup; no duplicate entry thereafter.
4. Monthly Payroll Processing
- LOP capture, salary revisions, arrears and full-and-final settlements.
- ECR upload, ESI challan and PT challan executed each month.
- Monthly TDS computation under Section 392 of the Income Tax Act 2025.
5. Form 16 and Annual Filings
- Form 16 Part B generated from Zoho Payroll; Part A reconciled from TRACES.
- Form 138 (old Form 24Q) quarterly filings and EPF annual return support.
- ESIC annual statements drafted and filed on your behalf.
6. Training and Handover
- Two structured sessions for HR / finance team - pay-run, ESS admin, reports.
- Troubleshooting playbook plus a 1-page quick-reference card.
- Optional quarterly health-check engagement available post handover.
Seven deliverables, signed off on go-live day.
Every Regikart Zoho Payroll engagement closes with a documented handover - the system, the SOPs and the training are all in your hands.
- Configured Zoho Payroll instance with statutory rules tested on a dummy pay-run.
- Salary structure template (Basic / HRA / Special Allowance / Reimbursements / Variable).
- Employee master sheet with UAN, PAN, ESI number, PT state mapping.
- ECR file template and EPFO portal upload SOP.
- First 2 pay cycles run alongside your team (with reconciliation against your prior payroll).
- Form 16 generation SOP and TRACES merge procedure.
- Training recordings and a 1-page quick-reference card.
Common Zoho Payroll setup challenges - and how Regikart solves them
Mid-year migration breaking TDS projections
Switching payroll software mid-FY without importing prior-month YTD figures causes Zoho Payroll to under-deduct or over-deduct TDS in the remaining months. Regikart reconciles your existing payroll register and imports YTD earnings, deductions, exemptions and TDS-paid figures before the first live pay-run.
Multi-state PT and LWF complexity
Maharashtra, Karnataka, West Bengal, Tamil Nadu, Gujarat and 11+ other states each have different PT slabs and LWF rules. We map each employee to their state of employment, configure state-wise registrations, and validate the slabs against current state notifications.
ECR upload rejection from EPFO portal
UAN mismatches, KYC pending status or wage type errors cause the EPFO Unified Portal to reject ECRs. We pre-validate every UAN against EPFO records and resolve KYC gaps before the first ECR is generated.
Form 16 reconciliation with TRACES
Zoho Payroll generates Form 16 Part B from the in-system salary data, but Part A must be downloaded from TRACES after Form 24Q is processed. Regikart trains your team on the download-and-merge SOP and provides a quarterly reconciliation between Zoho Payroll TDS, 24Q filed amounts and Form 26AS reflected.
Seven steps from organisation profile to first live pay-run.
Organisation Profile
Enter legal name, registered address, industry, work locations (head office plus branches). Choose whether this is your first payroll of the FY or a mid-year migration. Mid-year migrations require prior-year YTD imports for accurate TDS computation.
Tax Information
Enter PAN, TAN, TDS Circle / AO Code, and Tax Payment Frequency (monthly is the default for most businesses). These details populate the Form 16 and 24Q outputs.
Pay Schedule
Configure pay frequency (monthly is standard in India), pay date (last working day or 1st of next month), work-week (5 or 6 day), and the LOP calculation basis (actual days vs fixed 30-day basis).
Statutory Components
Enable EPF, ESI, PT, LWF in Settings > Statutory Components. Enter EPF establishment code, ESI sub-code, and state-wise PT registration. Select PT state to load the correct slab.
Salary Components and Structure
Build earnings (Basic, HRA, Special Allowance, reimbursements, variable pay) and deductions. Basic is typically 40-50% of CTC - higher Basic increases PF contributions but also expands HRA exemption ceiling under Section 10(13A).
Employee Onboarding
Import the employee master (CSV) with PAN, UAN, ESI number, joining date, salary structure, PT state, regime choice (Old vs New). Validate UAN against EPFO and PAN against Income Tax records.
First Pay-Run, Integration, and Sign-off
Run a dummy pay-cycle, reconcile contributions, generate the ECR, post to Zoho Books via the integration, distribute payslips through the ESS portal. Once reconciliation matches, the live first payroll goes out.
What you share at onboarding
Entity and statutory registration
- Company PAN, TAN and Certificate of Incorporation / LLP Agreement.
- EPF establishment code (or pending registration evidence).
- ESI sub-code (state-wise if multi-location).
- Professional Tax Registration Certificate (PTRC) and Enrolment Certificate (PTEC) - state-wise.
- LWF registration number (state-wise where applicable).
Employee and salary data
- Employee master: name, DOB, joining date, PAN, UAN, ESI number, bank account, salary structure, designation, work location.
- Prior-year YTD payroll register (for mid-year migrations).
- Salary structure policy document, leave policy and reimbursement policy.
Banking and reconciliation
- Bank account for salary disbursement (ICICI Bank, HSBC or YES Bank for direct integration; manual NEFT for other banks).
- Last 3 months of EPF / ESI / TDS challans for reconciliation.
Fixed-fee setup, no surprises.
Regikart fees are charged separately from the Zoho Payroll subscription (which is paid directly to Zoho Corporation). Final amounts depend on employee count, multi-state complexity and customisation depth.
Starter Setup
Up to 10 employees, single state
Statutory setup + dummy pay-run + Zoho Free plan
Standard Setup
Up to 50 employees, 1-2 states
Starter + multi-state PT + Zoho Books integration + first live pay-run
Professional Setup
50-200 employees, multi-state
Standard + Form 16 SOP + Zoho People sync + 2 training sessions
Managed Payroll
Outsourced pay-runs after setup
Monthly LOP + ECR + ESI + PT + TDS computation + payslips
All fees and charges listed are indicative only and do not constitute a binding offer. Final amounts may vary depending on the volume of work and the complexity involved.
Zoho Payroll subscription (paid directly to Zoho)
Reference pricing from Zoho Payroll India. Subscription billing is separate from Regikart implementation fees.
| Plan | Employees | Annual rate | Add-on per employee |
|---|---|---|---|
| Free | Up to 10 | Rs 0 | N/A |
| Standard | Up to 25 included | Rs 1,000/month | Rs 40/employee/month beyond 25 |
| Professional | Up to 50 included | Rs 2,000/month (approx) | Rs 50/employee/month beyond 50 |
| Premium | Up to 100 included | Custom | Custom |
Talk to a Regikart CA today for a fixed-price quote. Our team is available Mon-Sat 09:00-19:00 IST.
From discovery to first live pay-run - 7 to 14 working days.
| Milestone | Time |
|---|---|
| Discovery and requirements | 1-2 working days |
| Statutory configuration and salary structure | 2-3 working days |
| Employee master import and UAN/PAN validation | 1-2 working days |
| Integration with Zoho Books / Zoho People | 1 working day |
| Dummy pay-run and reconciliation | 2 working days |
| Live first pay-run + training | 1 working day |
| Total (standard) | 7 to 14 working days; 21+ days for multi-state or 200+ employees |
Statutory deadline tie-ins: payroll must produce ECR by the 15th of the following month for EPF, ESI challan by the 15th, PT challan by the 10th-21st depending on state, and TDS deposit by the 7th of the following month.
Three reasons the work holds up to EPFO and TRACES.
CA and CS expertise
Statutory compliance configured by qualified professionals, not just software installers. Every EPF establishment code, ESI sub-code and PT registration is verified against the underlying Acts before go-live.
Audit-ready records
Every ECR, challan and journal entry is reconciled and documented. Single point of contact at Regikart handles Zoho support, EPFO escalations and ESIC queries on your behalf - your team is not the project manager.
Penalty avoidance
Missed EPF deposits attract damages up to 100% under Section 14B of the EPF Act. Correct setup eliminates that risk. Average client saves 8-12 hours of HR / finance time per month after go-live.
“Regikart migrated our payroll from a legacy desktop system to Zoho Payroll over 12 days, including reconciliation of 8 months of YTD data for 78 employees across 3 states. The first live pay-run matched our prior payroll to the rupee. Quarterly TDS reconciliation now takes 2 hours instead of 2 days.”
Finance Head, manufacturing company, Pune (78 employees)
“We onboarded with Regikart for Zoho Books and added Zoho Payroll the next quarter. The integration means salary journals post automatically and our auditor signed off the payroll module without a single follow-up query.”
Founder, SaaS startup, Delhi NCR (22 employees)
Across Zoho Payroll engagements in FY 2025-26, Regikart delivered zero late EPF deposits, zero rejected ECRs after the first live cycle, and an average HR-time saving of 11 hours per month per client.
With offices in Kolkata (HQ), Delhi and Bengaluru, Regikart serves businesses across India both in person and remotely.
250+ clients served · 10+ years CA + CS practice · 3 offices · Zero late EPF in FY 2025-26
Four payroll options compared - line by line.
| Parameter | Zoho Payroll | GreytHR | Keka HR + Payroll | Manual / Excel |
|---|---|---|---|---|
| Starting price (India) | Free up to 10 emp | Rs 3,495/mo (15 emp) | Rs 6,999/mo (50 emp) | Rs 0 (time cost high) |
| PF / ESI / PT automation | Yes - native | Yes | Yes | Manual |
| TDS u/s 392 computation | Yes | Yes | Yes | Manual / risky |
| Form 16 Part B | Yes - in-system | Yes | Yes | Manual |
| Accounting integration | Native Zoho Books | Tally / QuickBooks | Multiple | None |
| ESS portal | Yes | Yes | Yes | None |
| Best for | Zoho ecosystem; 1-500 emp | Compliance-heavy mid-size | HR-tech first orgs | 1-3 employee firms |
The statutes Zoho Payroll automates against.
Indian payroll is governed by multiple parallel statutes - software does not change your statutory obligations, it only automates the calculation and filing workflow.
EPF and MP Act, 1952 (EPFO)
Provident Fund deductions, employer contributions, EPS share, monthly ECR filing and annual returns under the Employees Provident Fund and Miscellaneous Provisions Act, 1952.
ESI Act, 1948 (ESIC)
Health and disability insurance contributions for employees earning up to Rs 21,000 per month; employee 0.75% and employer 3.25% of Gross Pay.
State Professional Tax Acts
PT slabs and deposit frequency vary by state - for example, the Maharashtra State Tax on Professions, Trades, Callings and Employments Act, 1975.
Income Tax Act 2025 - Section 392
TDS on salary income; quarterly Form 138 (old Form 24Q) filings and annual Form 130 (old Form 16) issuance to every salaried employee.
State Labour Welfare Fund Acts
Small employer plus employee contributions to state welfare boards in 16+ Indian states; usually deducted half-yearly or annually.
Code on Wages, 2019
Replaced the Payment of Wages Act, 1936 from 21 November 2025. Timing and mode of wage payment and permissible deductions; impacts pay-cycle design and salary disbursement workflow.
Code on Social Security, 2020 - gratuity
Replaced the Payment of Gratuity Act, 1972 from 21 November 2025. Gratuity on separation after 5 continuous years of service, and after one year for a fixed-term worker; impacts full-and-final settlement workings in Zoho Payroll.
Code on Social Security, 2020 - maternity benefit
Replaced the Maternity Benefit Act, 1961 from 21 November 2025. Paid maternity leave entitlement; impacts payroll calculations and statutory compliance for female employees during leave.
- Late PF deposit attracts damages up to 100% under Section 14B of the EPF Act 1952, plus interest at 12% per annum under Section 7Q.
- Late ESI deposit attracts simple interest at 12% per annum under Regulation 31A of the ESI (General) Regulations 1950.
- Late TDS deposit attracts interest at 1.5% per month under Section 398(3)(a)(ii) of the Income Tax Act 2025 (Section 201(1A)(ii) of the 1961 Act), plus a penalty of up to the TDS amount (Section 271C of the 1961 Act for earlier periods).
- Failure to issue the salary TDS certificate (Form 130, old Form 16) on time attracts a daily penalty; under the 1961 Act it was Rs 100 per day under Section 272A(2)(g).
Official references: EPFO Unified Portal · ESIC Portal · Income Tax TRACES.
What Zoho Payroll executes - month after month.
| Recurring due date | What's filed |
|---|---|
| 7th of every month | TDS deposit for the previous month (Section 392) |
| 10th to 21st (state-wise) | Professional Tax challan for the previous month |
| 15th of every month | EPF ECR upload and ESI challan for the previous month |
| 31 July / 31 October / 31 January / 31 May | Quarterly Form 138 TDS return (old Form 24Q) |
| 15 June (annual) | Form 130 (old Form 16) issuance to all employees for previous FY |
| Half-yearly / Annual | Labour Welfare Fund contribution (state-wise schedule) |
| 31 May (annual) | EPF annual return (where applicable) and ESIC annual statement |
Why timely automation matters
EPF and ESI contributions must reach the respective authorities by the 15th of the following month - a single day's delay triggers interest at 12% per annum plus damages up to 100% under Section 14B of the EPF Act. TDS on salary must be deposited by the 7th of the following month; missing the deadline attracts interest at 1.5% per month under Section 201(1A). Every month without proper automation increases your exposure.
Zoho Payroll - answered.
Questions, answered.
If you don't see your question here, write to us and our team will get back to you.
Still have questions?
Tell us about your case and our team will walk through it and outline next steps.
Talk to our team →Quick answers
- Q: Minimum employees needed?
- A: One. The Free plan supports 1 to 10 employees at zero cost.
- Q: Works for proprietorships?
- A: Yes - any Indian business entity with employees on its rolls can use Zoho Payroll.
- Q: Direct salary disbursement?
- A: Yes via ICICI Bank, HSBC and YES Bank integration. Other banks use NEFT with auto-generated bank advice files.
- Q: Old vs New regime support?
- A: Yes - employees declare their regime in the ESS portal and TDS is computed accordingly.
- Q: Is data secure?
- A: Zoho lists ISO/IEC 27001 and SOC 2 Type 2 certification for all its cloud services, and names Zoho Payroll in its SOC 1 and SOC 2 + HIPAA reports (zoho.com/compliance). Access inside your payroll account is controlled by roles you set.
What pairs well with Zoho Payroll
Pair Zoho Payroll with these Regikart offerings for end-to-end finance and HR coverage.
Zoho Books Setup
Cloud-first books with GST built in - native integration with Zoho Payroll.
Payroll Outsourcing
Managed monthly pay-runs after setup - ECR, ESI, PT and TDS executed by Regikart.
TDS Return Filing
Form 138 (old 24Q) quarterly and Form 140 (old 26Q) for non-salary TDS - aligned with Zoho Payroll exports.
EPF / ESI / PT Registration
Pre-requisite registrations handled if missing before Zoho Payroll setup begins.
Go-live in 7 to 14 days, EPF by the 15th, TDS by the 7th - one CA accountable for the work.
Zoho Payroll combines Indian statutory compliance, native Zoho Books integration, employee self-service and Form 16 generation in a single cloud platform that scales from a 3-person startup to a 500-person enterprise. Correct configuration on day one is what separates a clean audit trail from a year of EPFO notices.
Setup starts at Rs 9,999 with a fixed 7 to 14 day go-live commitment for standard scopes. Our team is available Mon-Sat 09:00-19:00 IST.
Reviewed by CA & CS Team · Regikart · Last updated 26 May 2026 · Next review 26 November 2026