How do I add a stipend or benefit to an employee's pay in Zoho Payroll (US)?
Create the stipend as an earning component in Zoho Payroll's salary component settings, choosing whether it is taxable, then add it to the employee's salary details as a recurring amount or as a one-time payment in a pay run. For benefits like health or retirement plans, use the benefits or deductions settings so pre-tax treatment is correct. Confirm tax treatment with your accountant.
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In Zoho Payroll for the US, pay is built from components. Earnings cover regular pay, bonuses, allowances and stipends. Deductions and benefits cover items such as health insurance premiums and retirement contributions. Setting a stipend up as its own earning keeps it visible on payslips and reports, rather than burying it in salary.
Go to the salary component settings and add a new earning, for example remote work stipend. Choose how it is taxed. Some stipends are taxable wages, while reimbursements under an accountable plan may not be, so the rules matter. Then open the employee's profile and add the component to their salary with the amount and frequency. For a one-off payment, add it during the pay run instead.
Benefits work differently. A health plan or retirement plan usually involves an employee deduction, possibly pre-tax, and sometimes an employer contribution. Set these up in the benefits or deductions settings so taxable wages are reduced correctly. Exact menus can change, so check the current Zoho Payroll US help pages, and run a test pay run before the real one.
Key points
- Add a new earning component for the stipend in salary component settings.
- Set the tax treatment, with your accountant's advice.
- Assign it to the employee as recurring, or add it as a one-time pay run item.
- Set up benefits such as health or retirement plans as benefits or deductions.
- Preview the payslip in a test pay run before approving.
Common questions
Can I give a stipend only to some employees?
Yes. Components are added per employee, so only those who should receive it get it.
Will the stipend appear on the W-2?
Taxable earnings flow into wage reporting, so set the tax treatment correctly before the first pay run.
Sources and further reading
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Written by Flowpeak, a Zoho implementation partner. Zoho pricing and features change, so confirm current details on the official Zoho site. Free checklists | Ask us a question

