What gets withheld from a paycheck?

Quick answer: the usual things withheld from a paycheck

In most U.S. payroll, the money taken out of an employee’s paycheck typically falls into two buckets: (1) taxes and (2) certain benefits or deductions the employee agreed to.

Taxes commonly include federal income tax, Social Security (FICA), Medicare (FICA), and sometimes state income tax. Benefits commonly include things like health insurance premiums or retirement contributions (if the employee elected them).

Not every job has the same deductions. The exact amount depends on the employee’s pay rate, exemptions/elections, and your state’s rules. A payroll service should show the breakdown on each pay stub.

RunWise Pay is a free matching service (not a payroll provider), so we can help you find a payroll company that will calculate and file payroll taxes and keep your payroll compliant. You’ll still want to confirm specifics about your pay stubs and tax filings in writing with the provider you choose.

Taxes withheld (the main items): federal, Social Security, Medicare, and state

1. Federal income tax: This is withheld based on IRS rules and what the employee selected on their federal Form W-4 (for example, filing status and allowances/exemptions as applicable).

2. Social Security and Medicare (FICA): These are payroll taxes withheld from wages. Social Security applies up to a certain wage limit, and Medicare generally applies to wages without a wage cap.

3. State income tax (if your state has one): Many states withhold state income tax from employee wages, but the rules and rates vary by state. Some states have no state income tax.

Payroll timing matters: taxes must be calculated each pay period and then paid and reported to the right agencies on schedule. Deadlines vary and can change over time—so confirm the provider’s process and filing calendar.

Benefits and other deductions: what’s “withheld” besides taxes

Some deductions reduce the employee’s paycheck even though they’re not taxes. Common examples include health insurance premiums, certain retirement plan contributions, and other pre-tax or after-tax benefits depending on what’s offered.

Whether a deduction is pre-tax or after-tax changes how it’s treated for payroll tax calculations. For example, some retirement contributions may reduce taxable wages, depending on the plan type.

If you’re setting up payroll for the first time, ask your payroll provider to clearly explain how each deduction shows up on the pay stub—so you can verify the amounts match the employee elections and your benefit documents.

How to read a pay stub: look for the breakdown line-by-line

A pay stub usually shows: gross pay (before deductions), then each deduction category, then net pay (what the employee actually receives).

Common sections you’ll see include:
- Earnings (hours/days and rate, or salary)
- Pre-tax deductions (if applicable)
- After-tax deductions (if applicable)
- Tax withholdings (federal, Social Security, Medicare, and state if applicable)
- Net pay

If something looks wrong—like missing a tax type, a benefit showing the wrong amount, or year-to-date totals that don’t match—stop and compare against your employee’s W-4/benefit elections and your payroll provider’s report. Ask for the calculation details for that specific pay period.

If you’re switching payroll providers or fixing a payroll problem, a good provider will help reconcile prior pay runs and explain what will change going forward. Confirm in writing what support is included (for example, pay stub corrections, back-pay, and deadline handling).

Payroll red flags to watch for (especially if you’re new to U.S. payroll)

When you outsource payroll, watch for pricing and service problems that can lead to incorrect withholding or delays.

Red flags include:
- Vague pricing (no clear list of what’s included)
- Hidden fees (for tax filings, changes, corrections, or additional pay runs)
- No clear explanation of how they calculate withholdings and produce pay stubs
- Poor support or slow responses when you have a time-sensitive payroll issue
- Pressure to sign quickly without reviewing the agreement
- Claims of “guarantees” that aren’t specific (and aren’t backed by a clear process)

Before you sign, confirm what’s included in writing: tax filing responsibilities, pay stub reporting, year-end forms handling (W-2 and 1099 where relevant), direct deposit support, how changes to W-4/benefits are processed, and what happens if corrections are needed. Also check their turnaround times for amendments or missed filings.

Cost note: payroll services commonly charge a base monthly fee plus a per-employee fee, and sometimes higher fees for more pay frequency or additional services. Ranges often look like roughly $40–$100+ per month plus $4–$15+ per employee per month (not a quote), depending on state, pay schedule, and what’s included. Ask the provider to list everything line-by-line so there are no surprises.

How to get set up (or switch) with confidence using RunWise Pay

If you want a simple next step, start by matching with a payroll service that can handle the withholdings and filings for your business.

1. Use Get matched to share your business name, contact name, phone, optional email, how many people you pay, and your state.

2. Tell us your preferred language so you can work with a provider who communicates clearly.

3. Compare provider descriptions and ask the same written questions about withholding calculations, pay stub detail, tax filing responsibilities, and support for corrections.

RunWise Pay is free for business owners and is not a payroll provider—we help you find one. Don’t share employee SSNs, EINs, bank account numbers, or other sensitive records with us. We only collect contact and business intent details.

For more general help, browse Guides and Services to learn what payroll typically includes and how to plan for year-end.