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Set up tax exempt employees

Learn how to set up tax exempt employees in QuickBooks Desktop Payroll.

There are 2 kinds of taxes: company-paid and employee-paid.

  • Every tax calculated and tracked in QuickBooks is set up on the employee record and is added to employee paychecks, even when it isn't included in the employee's gross-to-net-pay calculation.
  • All company-paid taxes are added to paychecks but they don't impact net pay and aren't printed on pay stubs. They do, however, appear in payroll reports.
  • Taxes set up on an employee's record are calculated on the employee's paychecks. These taxes are added to the balance to pay for both company and employee-paid taxes. If the tax isn't set up on the employee record, it isn't added to the paycheck. Even if you add it to the employee record later, it isn't added on paychecks which have already been created.
  • How can I correct the numbers if I've done this?

    If you have made this mistake and need to correct it, run Payroll Checkup to fix the "wage base" for this tax, and on the next payroll, many straight-line percentage taxes (Medicare, SS, FUTA, SUI and SDI, but not FWH and SWH) will "catch up."

  • If you remove a tax from an employee, that employee will almost always be fully or partially excluded from any applicable tax forms including 941, 940, and your state tax forms (if you're an Enhanced Payroll service user).

It's almost never correct to remove a Federal or State tax from an employee's record. Here are the following situations where it's correct to exempt an employee from Federal or State tax or State selection on their record:

The employee lives or works outside of the US.

It's possible that the employee is subject to withholding in their home state, but since they work in another country, the SUI and/or SDI taxes aren't due on that employee. Check with your state agencies to be sure.

The employee has a special status.

For example, they aren't a U.S. citizen or are on a special visa. In this case, they are subject to some taxes and may be exempt from others. Read the rules carefully or get professional advice for this special situation.

The employee is working in a U.S. protectorate such as Guam.

In this case, QuickBooks doesn't support any "state-level" taxes for the employee directly. Leave the "state worked" and "state lived" blank, but set up any applicable local taxes as custom taxes, whether employee- or company-paid. QuickBooks supports both types of custom taxes.

The employer has a special tax-exempt status.

For example, a charity, church, or government organization may have a special status at the Federal or Dtate level. If you're sure you fall into this category, then deselecting some taxes may be appropriate.

Many employers make the mistake of removing a tax from the employee record when they shouldn't. Doing this incorrectly causes significant "downstream" problems that affect reports, tax forms, tax calculations, and liabilities due.

Common reasons why employers mistakenly remove a tax from an employee's record

The tax is company-paid.

QuickBooks knows which taxes are company-paid and which are employee-paid. All are added to the employee record based on "state lived" and "state worked," but only those that the employee pays are deducted from gross pay.

The tax rate is 0%.

Some employers confuse the case where the tax rate is 0% with being "not subject to" the tax. Typically, you're subject to a tax even when your rate is 0%, and you must report wages for the tax. If this is the case, you should include the tax on the employee's record, and set the rate to 0% on the Payroll Item list.

The employee claims "exempt" status.

Typically this means that the employee is claiming that they won't owe Federal or State withholding at year end due to hardship, high deductions, or low income status. This doesn't mean they aren't subject to the tax. "Subject to" and "exempt from" are two different but confusing concepts. For example, if you live or work in the US, you're usually subject to Federal tax. However, you may claim to be exempt from withholding. In this case, you should select "Do Not Withhold" as the withholding status.

My state doesn't collect this tax.

In QuickBooks, all employees who live or work in the US should have a "state lived" and "state worked" selected, even when the state doesn't collect that particular tax. For Enhanced Payroll service customers, this means that employees are identified with a state and are included on the state forms. Employee mailing addresses aren't used to determine an employee's locality.

The employee paid the tax while working for a previous employer this year.

In this case you're almost always required to withhold the tax again and the employee must file for a refund at the end of the year. You would also have to withhold tax even if the employee met the SDI and SUI limits while working for a previous employer.

I don't think I owe this tax.

For Federal and State taxes, this is unlikely. Almost all employers owe the taxes QuickBooks suggests.

The company has agreed to pay a tax that is usually paid by the employee.

This is a rare case. Even if it's correct, it's not supported by QuickBooks and your tax forms will be incorrect.

Follow the steps below to set up a tax exempt employee in QuickBooks Desktop Payroll.

Note: You must set up each exempt employee individually. You can't set up the company file as exempt from Federal and State taxes.

  1. Go to Employees, then select Employee Center.
  2. Double-click the name of the employee.
  3. Go to the Payroll Info tab.
  4. Select Taxes....
  5. Go to the Federal tab. From the Filing Status ▼dropdown, choose Don't Withhold.
  6. Go to the State tab. From the Filing Status ▼drop-down, choose the appropriate option. (The option will vary by state. You may see Don't Withhold, Exempt, or a different choice. If there's no Filing Status drop-down, your state is not subject to state withholding.)
  7. Select OK twice to save your selections.
  8. Repeat these steps for each exempt employee.

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