FAQs About Paying and Filing Taxes Through Zenefits Payroll

No. The Powers of Attorney forms you signed during setup authorize Zenefits Payroll to electronically sign these returns for you, so there's no need for you to handle or sign them yourself. Zenefits Payroll will transmit (electronically, or by paper where still required) the appropriate form to each state and Federal agency using the Tax IDs you provided during setup.

Sorry! Zenefits does not provide services related to the determination or payment of San Francisco's gross receipts or payroll expense taxes. These taxes depend largely on a company's corporate income, business considerations, and other corporate information that Zenefits does not handle.

Employers who conduct business in San Francisco should contact a tax advisor to determine their liabilty, if any, for the Gross Receipts tax.

More Information

San Francisco's Gross Receipts Tax Ordinance requires employers who engage in business in San Francisco, or have employees who engage in business in San Francisco, to pay a tax on their "gross receipts" in San Francisco. See the SF Treasurer's summary of the ordinance for more information.

The Tax Package can be found on the Reports tab of the Payroll app. It contains tax information for every jurisdiction (e.g., state, federal, or local) where employees had wages in Zenefits Payroll , detailed by tax type and amount.

  • For companies who elected to pay/file on their own in one or more jurisdiction, or those that were notified that Zenefits Payroll could not file or pay their taxes, the report will detail how much is due for each type of tax, and in which jurisdiction. These companies can use these details to complete the appropriate returns and file them with the respective agencies. See this page for contact information and websites for agencies sites in each state.
  • For all other companies, the package will detail the exact amounts reported and paid for each tax in each jurisdiction. Since Zenefits Payroll e-files in the majority of jurisdictions (a data exchange process that does not use the actual paper return forms), the tax report won't include PDFs of the actual returns or transmittals, but will include all the same information that would be used to complete state and Federal forms (e.g., Form 941, 940).

When you run payroll, Zenefits Payroll will debit employer and employee taxes for the run from your payroll account along with any reimbursements and employee net pay (for Direct Deposit). These amounts will stay in Zenefits Payroll's clearing house bank account until it's time to pay your taxes.

Some states and local jurisdictions also have periodic taxes, which aren't tied to your pay schedule(s). If you're subject to one of these periodic taxes, Zenefits Payroll will debit these taxes separately, towards the end of the period. Learn more.

For example, New York City's MCTMT tax is calculated on a quarterly basis, based on a company's quarterly payroll expenses. For companies subject to MCTMT, Zenefits Payroll will calculate and debit MCTMT taxes at the end of the quarter.

Your filing schedule in each state is determined by your deposit schedule in that state. 

  • In states without income tax, filing schedule is the same as deposit schedule.
  • State unemployment taxes are filed and paid on a quarterly basis in all states.
  • For states with more than one deposit frequency for income taxes, the rules for determining filing schedule using deposit schedule will vary from state to state. 
  • For Federal deposit schedules, payments are automatically sent in the first week. 
  • For employment/withholding schedules, the deposit schedule is assigned by the state and is specific to your company. 

In all cases, Zenefits Payroll will file the appropriate returns for each state or local jurisdiction in which your tax payments were made.

  • In the majority of states and local jurisdictions, these returns are filed electronically. In those that still require paper returns, Zenefits Payroll will fill these out for you.
  • During setup, you signed an authorization form for Federal taxes and one or more forms for State taxes. These forms allow Zenefits Payroll to file tax returns and deposit your taxes with the appropriate agency. There's no need for you to sign the forms; Zenefits Payroll will do that for you!
  • Once your returns are submitted, you'll be able to download a tax package in payroll (on the Reports & Forms page) that reports details on your returns.
Here's a list of each State's Payroll Tax and Registration Guide which includes rates, tax forms, required documentation, filing schedules and contact details.

Zenefits Payroll deposits state and local taxes other than unemployment according to the deposit schedule you selected for each state during setup, or the schedule mandated by the jurisdiction (e.g., when there's only one schedule). All state unemployment taxes are deposited on a quarterly basis. Here's a list of deposit schedules for each type of tax in each state.

If permitted by a particular agency, Zenefits Payroll will make early deposits.

To check your current schedule for a particular state, click the Payroll app, then click Settings, then Taxes and find the particular state in the list.

Zenefits Payroll determines which taxes a company (and their workers) should pay using the work locations and home addresses of each. For each unique state where at least one person lives or works, Zenefits Payroll will withhold individual and company taxes for that state, even if the company has no physical location in that state or has never paid taxes in that state before.

Please contact Zenefits Customer Care to let us know:

  • If you believe that you or your workers are being taxed incorrectly.
  • If you do not want Zenefits Payroll to withhold taxes in that particular state.

It's important that we know to ensure that your employees' W-2s and your returns are accurate.

If you've been notified that Zenefits Payroll will be refunding to you taxes that were withheld in one or more state jurisdictions, it's mostly likely because you didn't provide us with the necessary state tax IDs that we would use to make your payments or file your taxes in those jurisdictions. You will be set to Calculate Only if you do not provide the required information. You'll need to make these payments on your own, and file returns for these payments as well. See this page for specific instructions.

Quarter's-end tax reconciliations are an industry-standard practice used by payroll providers to make sure that that the the taxes collected in the quarter's payroll runs match up with the amounts expected by state and Federal agencies, and to ensure that all tax payments and filings are correct and timely. 

In some cases, we'll find variances between these two amounts. Most variances are small, and due to corrections, reversals, or changes to tax rates. For example, state unemployment agencies will reevaluate companies' unemployment tax (SUTA) rates on a yearly basis, assign new rates at the beginning of the year, and communicate these rates via tax notices. After the rate is updated in payroll, reconciliations help to correct any variance so that payments and returns can be updated.

If we do find a variance, we'll add a reconciliation run to your payroll.

  • You'll be able to spot one of these runs because it has $0 for taxes and earnings. You won't be able to edit it.
  • Runs may be added for over or underpayment alike. If there's an underpayment, you'll see a run for a positive amount. If you overpaid, you'll see a credit.

  • Reconciliation runs will be processed automatically in mid-month at the end of each quarter (April, July, October, and December for end of year).

  • Going forward, you might see these runs again the next time Zenefits Payroll does quarter's end reconciliations.
If you wish to determine the details of a quarter end reconciliation debit:
  • Download an All-in-One report selected to Pay Period.
  • From the drop down, find the pay run labeled Quarter End Variance report or Quarter End Variance run.
If you receive a tax notice, make sure to contact Support and provide the notice. Zenefits Payroll will automatically perform reconciliations as necessary based on the notice.

If you see a pay run in Zenefits Payroll that has $0 for employee earnings, taxes, and deductions, but a positive or $0 total cost, it's simply a record of a reconciliation that Zenefits Payroll makes to balance your tax accounts.

  • If the total cost is a positive amount, Zenefits Payroll is making an extra tax payment. For example:
    • For a periodic employer tax, such as New York's MCTMT (quarterly) or Colorado's head tax (monthly).
    • For a reconciliation payment, e.g., if your company's tax rates changed during the quarter and Zenefits Payroll needs to bring your payments up to date.
  • If the total cost is $0, it's simply a reconciliation run that Zenefits Payroll is using to make your tax payments to the state/federal agency.

If you received a notice from Zenefits Payroll payroll that you're responsible for filing and paying state payroll taxes yourself, it's because:

  • Our system withholds taxes in every jurisdiction where your employees live and work (determined by your employees' work locations and addresses), and
  • Zenefits Payroll did not receive the appropriate state tax IDs that we needed to pay and file these taxes for you.

Since the deadline for you to provide your tax information for the quarter that's about to close has passed, Zenefits Payroll can no longer file your taxes in those states.

  • You’ll need to file and pay in the jurisdictions in question yourself. See this page to learn more about filing and paying on your own.
  • Zenefits Payroll will still file your federal taxes, since you provided your federal EIN at setup.

The federal R&D tax credit, also known as the Research and Experimentation (R&E) tax credit, is intended to reward U.S. based companies to increase their investment in R&D for the current tax year. 

At this time Zenefits Payroll cannot support it. 

What are these forms? 

Form 6765 is a tax credit for increasing research and Form 8974is a specific small business tax credit for increasing research. A qualified small business that elects to claim the payroll tax credit will claim the payroll tax credit against the employer’s portion of social security tax on its employment tax return for the first quarter that begins after it files the return reflecting the payroll tax election. A qualified small business claiming the payroll tax credit on its employment tax return must complete Form 8974

What happens if we file it on our own? 

If you do, we will not be able to assist with any tax notices that come as a result and we cannot confirm that the federal filings will be correct.



If you receive a tax notice stating your withholding rate, or tax deposit rate, has been changed by the jurisdiction, you will need to update the rate in your payroll account.

To do this, go into your Payroll App then click on Settings.  On the left-hand side, click into Taxes (Federal & State), then edit for the state that needs to be updated. Zenefits does not automatically update this information. You are responsible for keeping your company's tax rates and tax deposit schedule updates in the Zenefits system.


An in product walk through is also available to guide you step by step in Zenefits. 

Still need our help? Our support team is waiting to help you. Contact us