My company operates in Florida. I am hiring an employee that will work remotely and lives in NY. Do I need to withhold NY or FL Taxes?

Hi @amfe-bellsouth-n , i think tax based on work location so it's FL taxes. Comment back, cheers.

Hello there, @amfe-bellsouth-n.

I'd like to ensure that you'll be able to withhold the accurate state tax for your employee in QuickBooks Online.

Some states have reciprocity agreements. A reciprocity agreement between states means that the employee only pays taxes in one of the state, which is the state where the employee lives. 

To get this issue sorted out, I recommend consulting your state agency to determine what income taxes you may be subject to. Here's a link that will give you further clarifications regarding the multi-state employment payroll situations: Learn the things you need to know if you have multiple work locations in different states.

I'm also adding these references below about the actions that you need to take to identify your withholding responsibilities and on how the system calculates taxes:

• Guidelines to assist you with determining withholding responsibilities specific to supported QuickBo...
• Learn how QuickBooks calculates taxes to understand the tax amounts reported on an employee's payche...

You can always get back to me here if you have any other questions about this or with QuickBooks. I'm always up for further assistance. Take care!

The OP is using QuickBooks desktop, so your answer does not appear to be pertinent.

It depends on whether or not having an employee who lives and works in NY creates a "Nexus" for your company in NY. It probably does and if so you will have to register as an employer in NY and withhold taxes for NY, but there may be an exception for NY.  It's tricky:

See https://www.wipfli.com/insights/articles/tax-covid-19-remote-employee-nexus

Individual income tax payment and withholding

"For state individual income tax and related payroll withholding purposes, employees’ wages for the performance of personal services are generally sourced to the state where they performed work. 

In the case of telecommuters, this generally means that payroll withholding is due to the state from which they telecommute, regardless of the location of the employer. However, for certain states and cities that have adopted the so-called “Convenience of the Employer” test (Connecticut, Delaware, Nebraska, New York, Pennsylvania and Philadelphia), the wages of remote workers are still sourced to the employer’s location unless the employee can demonstrate that the remote working arrangement was done for the employer’s necessity, not the employee’s convenience."

See also https://pro.bloombergtax.com/reports/2018-state-nexus-policies-and-payroll/

It's really important to get this right, so I recommend consulting a payroll tax professional or contacting NY state.