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Payroll · New York

Best Payroll Software for New York Businesses

New York employers handle federal, state, and city income tax in one pay run. Yonkers surcharges, Paid Family Leave, and the MTA Payroll Mobility Tax add more layers. Keka helps businesses in New York keep payroll accurate and compliant every cycle.

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PAYROLL COMPLIANCE

Stay compliant with New York payroll requirements

One payroll flow for time, leave, and attendance.

Attendance, leave, and timesheets sync directly into payroll. No exports, no reconciliation, no mid-cycle corrections.

No compliance surprises on payday.

New York State and NYC tax rules, minimum wage tiers, FLSA overtime requirements and deduction caps are handled — before errors reach a paycheck.

Built for multi-location New York teams

Run payroll across NYC and New York State with location-based rules, pay rates, and compliance handled in the same payroll flow.

WHY NEW YORK PAYROLL IS DIFFERENT

State, city, and local taxes stack up in New York

New York has several tax layers, and each one depends on where the employee lives or works. One missed jurisdiction creates a compliance gap. Keka applies each layer to the right employee automatically.

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Federal income tax

Federal withholding applies first, with standard FICA included for all covered employees.

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New York State income tax

New York uses a progressive state tax system with 9 brackets, ranging from 3.9% to 10.9%.

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New York City income tax

NYC residents face an additional city income tax, ranging from 3.078% to 3.876%.

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Yonkers surcharge

Yonkers residents owe an additional surcharge equal to 16.75% of New York State tax liability.

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New York Paid Family Leave

New York Paid Family Leave is employee-funded at 0.432% of gross wages, subject to an annual cap.

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MTA Payroll Mobility Tax

Employers in the 12-county MCTD region may owe the MTA Payroll Mobility Tax. The rate depends on location and payroll size.

MULTI-LOCATION PAYROLL

Run payroll accurately across New York locations

Keka’s US payroll engine maps each employee to their pay group and work location, helping apply the right tax and wage rules automatically.

Supports location-based rates for New York City, Yonkers, and other New York locations
Lets you configure state and local deductions, including programs like Paid Family Leave, disability, and regional payroll taxes
Approved timesheet hours sync directly — no manual entry

PROACTIVE COMPLIANCE

Payroll errors flagged before every pay run

Keka surfaces missing tax setup, non-compliant wage rates, and incomplete configuration before every run — each with a direct fix.

Missing tax setup and FEIN verification flagged before processing
Pay below New York State minimum wage blocked before saving
Every alert links directly to the step that resolves it

COMPENSATION MANAGEMENT

Multiple pay rates, piece-rate, and 401(k) — one place.

Set different rates by role, shift, or location. Keka applies the correct rate to every paycheck without manual intervention each cycle.

Per-hour, per-annum, and per-piece pay types natively supported
Different rates across roles, shifts, and New York locations in one record
401(k) contributions auto-deducted and synced with providers like Guideline

SECURITY, SCALE & RELIABILITY

Built for scale.  Trusted for security.

Keka stays updated with every federal, state, and local payroll rule – so you never worry about tax changes or compliance gaps.

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Keka is not just an HRMS. It’s our operations backbone. From admin to board-level reporting, we rely on it every day. Payroll used to take 5-7 days. With Keka, it’s done in just 2-4 hours.

Biren Kumar Dash

Vice President - Varmora

Keka has helped us increase transparency and trust across the organisation. This is now our source of truth for people intelligence.

Elizabeth Joseph

Director of People and Culture - Land Sterling

Keka helped our managers in building accountability, empathy and it really made a difference in creating a very collaborative culture. Keka also surpassed our employee expectations with its easy-to-navigate UI and simple dashboards.

Rahoul Srivastav

HRBP - Noise

Workforce Planning Highest User Adoption

Full New York compliance coverage

New York payroll compliance coverage for every tax layer

New York requirement	What Keka does	How it helps
NYC & upstate minimum wage $17.00/hr NYC · $16.00/hr upstate	Validates pay rate against work location before saving	Flags violations
New York Paid Family LeaveEmployee-funded · 2024 rate: 0.432%	Calculates capped PFL deductions and reflects them on pay stubs.	Auto-deducted
State Disability Insurance0.5% of wages, max $0.60/week	Calculates SDI deductions using configured weekly or per-period caps.	Auto-deducted
New York City income taxProgressive rates · NYC residents only	Withholds based on residential address and bracket	Auto-withheld
Yonkers income tax surcharge16.75% on New York State liability	Detects Yonkers residency; applies surcharge automatically	Auto-withheld
MTA Payroll Mobility TaxMCTD employers above $312,500/qtr	Applies regional payroll taxes based on pay groups and locations.	Auto-calculated
New York State overtime 1.5x after 40 hrs/week	Synced from approved timesheets; no manual calculation	Timesheet-synced

INTEGRATIONS

Plugs into the finance and HR stack you already run

QuickBooks

Sync payroll journal entries to your QuickBooks chart of accounts each cycle.

Xero

Auto-map deductions, taxes, and benefits to your Xero accounts.

NetSuite

Push payroll runs, headcount, and accruals into your NetSuite general ledger.

Sage Intacct

Send each pay cycle's data into Sage Intacct without manual exports.

Guideline

401(k) contributions deducted and remitted to Guideline every pay run.

Slack

Payroll approvals, alerts, and error flags delivered to your Slack channels.

Okta

Single sign-on and SCIM user provisioning across the Keka platform.

Keka Marketplace

50+ more apps across HR, finance, and operations.

Compliance Library

New York payroll and compliance resources

Stay current on New York employment law.

New York Overtime Laws New York Minimum Wage 2026 New York Lunch Break Laws New York Leave Laws New York Paycheck Calculator

Frequently Asked Questions

Can Keka handle payroll for both New York City and upstate employees in the same account?

Yes. Keka supports location-based pay rates and calculates earnings and taxes in a single payroll flow for New York employees.

Does Keka automatically calculate local income taxes for New York employees?

Keka supports local tax withholding within US payroll, including calculations alongside federal and state taxes for New York employees.

How does Keka handle New York Paid Family Leave deductions?

Keka can support New York Paid Family Leave deductions within payroll, so contributions are calculated according to configured deduction rules.

What happens when I hire a new employee in New York — what does Keka take care of?

Keka helps centralize New York wage and tax information for new hires and supports configured templates and payroll settings.

Can Keka help if I get audited by the New York Department of Labor?

New York employers are expected to keep detailed payroll and wage records for multiple years and provide them promptly during an audit. Keka centralizes payroll and employee records in one system with secure, searchable access, so if an audit happens you can quickly pull the reports and documents you need instead of digging through paper files or spreadsheets.

One payroll system for every New York payroll obligation

Federal, state, and local payroll requirements — handled automatically from start to finish.

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