Netchex launches Mesh AI HR Teammates for the Deskless Workforce

Learn More Arrow
Payroll Tax FAQ

Payroll Tax FAQ: Answers to the Questions Employers Ask Most.

Short, direct answers about how payroll tax works at Netchex. For the full picture, see Payroll Tax Filing Services and the Payroll Tax Onboarding Guide. The IRS explains the federal returns on Form 941 and Form 940.

Last updated: October 8, 2026

Payroll Tax Resources/Filing Services/Onboarding Guide/FAQ

Setup and responsibility

Will Netchex complete my state agency applications?
No. Business owners and administrators complete agency applications, because they request specific company information Netchex does not readily have. Once you are registered, send us the account numbers and rate notices and we handle the deposits and filings for full-service clients.
Does Netchex decide which taxes I need to withhold?
No. Owners and administrators set up employee tax withholding, including state withholding, unemployment, and any local taxes. We can offer written guidance from the American Payroll Association to support your decisions. We still recommend checking with your CPA or business attorney before you decide.
Does Netchex need my payroll tax account numbers?
Yes. Account numbers make sure payments and returns post to the right account. Many agencies no longer accept payments or returns without the correct number, and some assess penalties for paper returns or checks. Send every account number during onboarding so nothing is delayed.
What payroll tax documents should I send to Netchex?
Forward frequency changes, rate changes, deposit requirements, credit balances, notices of balance due, and notices of discrepancy through NetHelp so we can update your account. Netchex does not process corporate tax returns, including excise, sales, and franchise taxes. Those stay with you and your accountant.
Should I forward my quarterly and annual tax reports to Netchex?
If you are a full-service client, we file your quarterly payroll returns for you. If you receive blank payroll tax returns, you can forward them to the Tax Department through NetHelp. We will confirm the account numbers, frequency, and other details for accuracy.

Moving to Netchex

Will Netchex deposit federal and state withholding for payrolls run before us?
No. Federal and state taxes accrued before your transition to Netchex are remitted by your previous provider. If you believe those taxes were not paid on your behalf, submit a case to the Tax Department and include what you know about the dates and amounts.
Will Netchex pay unemployment taxes that my previous provider refunded?
Yes, for the quarter you start with us. SUTA and FUTA are paid and filed quarterly, so we deposit the full amount due for that quarter. Federal unemployment is due only when liability reaches $500, so your prior provider could also have refunded earlier quarters. Submit a case if that happens.
Will Netchex file quarterly reports for periods before we started?
No. We begin filing quarterly returns within the quarter your first payroll runs with us, and we do not process returns for earlier periods. Your previous provider stays responsible for those, so get copies of everything they filed and a deposit history.

Rates, frequencies, and deposits

Will Netchex retrieve my new unemployment rates?
Where it applies, we participate in the SUTA Rate Exchange, but sometimes we do not receive the rate. An expired POA, an agency that does not participate, or a different spelling of your legal name can be the cause. Agencies notify employers directly, so upload each rate notice in Tax Settings to update your rate.
How does Netchex assign withholding tax deposit frequencies?
If we do not receive your assigned state deposit frequency, we assign the most frequent one. Review your Tax Verification Report and tell us about any change right away, because some agencies assess penalties when deposits do not follow the assigned frequency. We keep the initial frequency until you notify us.
Does Netchex send a confirmation of each tax deposit?
Not for every deposit. Each quarter we provide a Reconciliation Recap that lists your liabilities against the deposits we made for you. If you need confirmation of one specific deposit, submit a case through NetHelp and ask the Tax Department to confirm it.
What should I do if I get a tax notice?
Send it to us right away through NetHelp. That includes notices of balance due and notices of discrepancy, along with any rate, frequency, or credit balance notice. The Tax Department reviews each one against your account, so keep the notice itself and any related agency correspondence ready.

W-2s and employee data

Will Netchex file W-2s for my terminated employees?
Yes. We file W-2s for every employee with a balance in a given year, so submit all payroll history, including terminated employees, with your balances. Missing data leads to incorrect payroll tax returns and W-2s, which are harder to fix after the fact.
Can data entered in Netchex affect my tax filings and W-2s?
Yes. The Tax Department reports directly from employee profiles and the payrolls you process. A misspelled name, an invalid SSN, or a wrong address can cause agencies to reject filings or W-2s. Verify employee data early, and correct any erroneous payroll data so federal and state reports are right.
Does Netchex process third-party sick pay or disability payments?
Yes. We include the data in your 941 reporting, collect and deposit the employer liability, and report it on Form W-2 if the provider does not. Ask your provider whether they report this information on year-end W-2 forms, so nothing gets reported twice or missed.

State and program questions

Does Netchex file and pay New York disability insurance (NYDI)?
New York requires employers to provide disability benefits coverage, through the NY State Insurance Fund or a private insurer. You collect the contributions from employees. The deduction is withheld from paychecks and credited back to you on each payroll invoice, so you can remit it to your insurance carrier.
How does Netchex handle Washington L&I?
Washington L&I is based on hours actually worked. Employers may use earnings codes for hours that are not productive time, such as paid time off, and Netchex cannot tell which of your codes reflect real work. Mark which earnings codes record productive hours so only those count toward L&I.
Does Netchex support private paid leave plans?
Yes. Private plans can be set up differently from state-sponsored programs. For a state program, we collect and pay premiums and treat the liability as a tax. For a private plan, the amount may be a payroll deduction that you remit to your provider. Confirm the setup with your implementation manager.

Still have a question?