Showing results for 
Search instead for 
Did you mean: 

New York Withholding Payments

This document outlines the special instructions you need to follow for QuickBooks if you are assigned Quarterly Frequency for Withholding by the New York Department of Revenue or if you are mandated to use PrompTax for all payments.

NYS-1 Payments

The quarterly payment frequency for NYS-1 is available in QuickBooks for electronic filing.

  • These payments are made Quarterly with the NYS-45 for payrolls where total accumulated tax withheld is less than $700.

If you accrue $700 or more in withholding liability, you must pay within 3 or 5 business days.

Make the first payment using the Quarterly Frequency.

  • After the initial payment is made, you MUST CHANGE your Deposit Frequency to 5 day for the rest of the Quarter. Use the same date (your paycheck date) for begin and end dates of the filing period.
  • Failure to do so could cause notices.

NYS-45 Impact to Withholding Payment

When you E-file and Pay your NYS-45 the filing and the UI payment are sent together. The Withholding payment is a separate transaction.

  • If you owe withholding, you must send the withholding payment separately from the NYS-45.
Note: The NY Withholding Identification Number is pulled from the Account ID box in the NY-Withholding payroll item inside QuickBooks.  The final number in the sequence, the number that comes after the space in the ID number, will not always match the number on the payroll item.  This number is called a check digit, and when used on NY tax forms, is a calculated number derived from the other numbers in the ID.  For more information, see page 7 of the Specifications for Reproduction of New York State Employment Forms.

Alternative Submission Process

If you are unable to submit through Intuit, you can file directly with the New York Department of Taxation and Finance through the services you are mandated to use. The Tax Department notifies you vial email if you're required to submit via Web File or PrompTax.

Submit via Web File

Use the Web File service to file NYS-1 unless you are mandated to use PrompTax.

  • To use Web File, you must have an online service account. Go to the Web File service site for information on how to create your account.
  • After enrolling to the service, store your User name and password in a secure location. You will need these informaion every time you e-file and e-pay through the Web File site.

Submit via PrompTax

PrompTax is an electronic filing and payment program that's mandatory for certain businesses. Failure to file through PrompTax when you are notified too, will incur penalties.
Withholding tax filers whose aggregate tax withheld through Form NYS-45, Quarterly Combined Withholding, Wage Reporting, and Unemployment Insurance Return, filed for the previous tax year that is $100,000 or more must enroll in this program.
  • To  use PrompTax, go to the PrompTax site for information on how to enroll.
  • Store your Access code and password in a secure location. You will need these informaion every time you e-file and e-pay through the PrompTax Program.


Was this helpful?

You must sign in to vote, reply, or post
Sign in for the best experience
Ask questions, get answers, and join our large community of QuickBooks users.
Sign In / Sign Up

Need to get in touch?

Contact us