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FAQs About Running Payroll in Zenefits Payroll

When is payroll due in Zenefits Payroll?

In Zenefits Payroll, pay runs must be submitted by 2 :00 PM PST on your company's processing deadline date. The approval date will be 4 business days or 2 business days before the check date, depending on your block period.

  • This deadline leaves enough time for Zenefits Payroll to debit funds from the company's bank account and transfer them to employees' banks, and for banks to process the transfer and deposit the funds in employee accounts. Employees should receive their deposits on check date, but delays may occur for particular banks.
  • Off-cycle pay runs are subject to the same deadline, so if you usually run payroll 4 days before check date, your off-cycle runs will have check dates that are 4 business days after you submit the run.

For example, let's assume you have semi-monthly payroll, and check dates of the 15th and last day of the month.

  • If the next pay date is April 15th, run payroll on the 11th by 2 :00 PM PST.
  • Zenefits Payroll will debit your account on the evening of the 11th.
  • Deposits should post to your employee's accounts on the 15th.

How do holidays and weekends affect pay periods in Zenefits Payroll?

During holidays that are deemed a “banking holiday,” banks will not process pay runs and will not send direct deposit payments. The ACH only sends direct deposit payments on weekdays; this means pay runs and payments will not be processed on weekends or on holidays that fall on a weekday.

You may submit payroll on a holiday or weekend, but Zenefits Payroll cannot process transactions on holidays or weekends.

Holidays and Weekends in Zenefits Payroll

If a pay run's check date falls on one of the banking holidays, or on a weekend, the run's check date will be moved before or after the holiday or weekend, according to your company’s weekend and holiday rule

Please note: the deadline to run payroll and reminder emails will be prorated accordingly. For example, if a pay run's deadline moves to a day earlier than you would normally run it, you will still receive reminders to run payroll three (3) days, two (2) days, and one (1) day before the new approval date. 

In the event that your pay period ends on a banking holiday or weekend, you may approve and push the hours that have been submitted and pay out the missing hours in a separate, off-cycle run, or simply add them to the next pay period. 

How do I reset a pay run in Zenefits Payroll?

You can refresh a Draft pay run by clicking the three stacked dots in the upper right corner of the people table and selecting Reset Run. If you accidentally Delete a regular run, contact Zenefits Customer Care to have it regenerated.

How do I make a change in a single paycheck?

To make a one-time change to a single paycheck for an employee in Zenefits Payroll, make the change directly in the  paystub for a particular run:

  1. Click Pay Runs.
  2. Click the name of the run in the Drafts list.
  3. Click Edit Paystub for that individual.
  4. Make the change, then scroll down and click Save.

How do I make a change to future paychecks?

To make a permanent change that applies to all of an employee's future paychecks, make the change in the employee's pay template.

How do I add reimbursements in Zenefits Payroll?

You can add both one-time and recurring reimbursements in Zenefits Payroll.

  • One-time reimbursements should be added directly to the employee's paystub in a pay run.
  • Recurring reimbursements should be added to the employee's pay template so that when Zenefits Payroll generates future runs, the reimbursement is automatically added to the employee's paystub.

If you'd like to create a custom-named reimbursement type, e.g., a travel or cell phone reimbursement, see these instructions. For more information, see this Help Center guide to managing employee earnings in Zenefits Payroll.

How do I pay hourly workers in Zenefits Payroll?

Companies who want to pay hourly workers in Zenefits Payroll can use Time & Attendance to automatically add hours to payroll.

  • Time & Attendance is optional for hourly workers.
    • Hours for workers who don't use Time & Attendance can be manually entered in individual pay stubs in each run.
    • Zenefits Payroll will generate separate pay runs for workers who use Time & Attendance and for everyone else (those salaried and those who are hourly but do not use Time & Attendance, even if all workers have the same pay frequency.

How do I automatically enter hours into Zenefits Payroll?

If your hourly employees use Time & Attendance, their hours will automatically be entered into payroll. Learn more about using Time & Attendance with Zenefits Payroll.

If they don't use Time & Attendance, you can enter their hours into their pay templates and have those hours automatically added in each pay run:

  1. First, follow these instructions to create a custom earnings code using the Regular Earnings category. Rename it something other than "Regular Earnings."
  2. For each hourly employee, follow these instructions to add their normal number of hours per period (e.g., in a week) to their pay template. Use the earnings code you just created instead of "Regular Earnings."

If you choose the latter, remember that the number of hours you to their pay template will always be added to their paystub. If an employee were to work less than the normal number of hours in one pay period, you'll need to edit those hours manually in the employee's paystub for that run.

How do I correct a completed pay run in Zenefits Payroll?

Please contact Support to make corrections to a pay run after it is processed for payment. Make sure to provide the check date(s) for the affected run(s), the names of affected people, and an explanation for the request so that Zenefits Payroll can create the run for you and provide more instructions. Here's an explanation of the process.

How do I create a final check in Zenefits Payroll?

When completing the termination details in Zenefits for an employee paid through Zenefits Payroll, make sure to select "Yes" when Zenefits asks if you'd like to mark the employee as terminated in payroll.

  • If you need to pay the employee sooner than their next regular pay date, remove them from the next regular pay run and then run an off-cycle termination payroll. You'll need to manually enter all earnings, but you can have Zenefits Payroll include normal deductions and contributions.

For more information, see this guide to terminations in Zenefits Payroll. Remember that state regulations for last paychecks vary, and some states (e.g., CA) require you to provide employees with their final paycheck on their last day.

How is total cost calculated for pay runs?

The total cost of a pay run includes net pay, employee and employer taxes, deductions and contributions, and reimbursements:

Total Cost = Gross Pay + Contributions + Employer Taxes + Reimbursements

For example, consider a pay run with two employees (with no contributions):

  Gross Pay Deductions Employee Taxes Employer Taxes Net Pay Reimb. Cost to Employer
Worker 1 5000 300 1606.18 552.25 3093.82 100 5652.25
Worker 1 3000 200 854.75 329 1945.25 50 3379
Totals 8000 500 2460.93 881.25 5039.07 150 9031.25
  8000 + 881.25 + 150 = 9031.25

However, the actual amount withdrawn to pay the run may be less, especially if some employees are paid by check. Learn more.

Why do my bank debit amounts differ from a run's total cost in Zenefits Payroll?

The amount that Zenefits Payroll will debit from your company's payroll account includes net pay and reimbursements for employees paid by Direct Deposit and employee/employer taxes.

Zenefits Payroll uses this equation to calculate the total amount withdrawn from your account:

Total Debit = Net Pay and Reimbursements (by Direct Deposit) + Employee Taxes + Employer Taxes

This debit amount does not include employer contributions, employee deductions, or any net pay amounts paid by manual checks. Consequently, the actual debit may be less than the total cost of the run.

For example, consider a pay run with two employees:

  Gross Pay Deductions Employee Taxes Employer Taxes Net Pay (DD) Cost to Employer
Employee 1 5 ,000 300 1606.18 552.25 3093.82 5252.25
Employee 2 3 ,000 200 854.75 329.00 1945.25 3129.00
Totals 8 ,000 500 2460.93 881.25 5039.07 8881.25

The total cost is:

  8 ,000   + 881.25   8881.25

The total debit is:

      2460.93 + 881.25 + 5039.07 = 8381.25

When does Zenefits Payroll withdraw funds from my bank account?

Zenefits Payroll will initiate the debit to your company's payroll account on the evening that payroll is due, as long as you have approved the pay run. 

If you submit payroll prior to the day that payroll is due, Zenefits Payroll will not initiate the debit to your company’s payroll account until the evening that payroll is due, as long as you have approved the pay run.  

This is to ensure you have enough time to unapprove and edit the run, if necessary.

When payroll is approved, you will want to ensure there are enough funds to cover the employee deposits and taxes for the run submitted.  

Why is my payroll account debited twice for each pay run?

Zenefits Payroll will perform two separate debits for each pay run. One debit is for the wages paid via direct deposit and the other is for payroll taxes in full. This keeps Zenefits Payroll in line with standard industry practices, and provides additional payroll visibility.

Why didn't a worker receive their direct deposit?

Direct Deposit transfers can take 1-2 banking days from check date to post to individual bank accounts; times for individual banks will vary. Any Direct Deposit funds transferred by Zenefits Payroll that don't successfully post to a valid bank account within 5-7  banking days will be returned to your payroll account. If someone doesn't receive their Direct Deposit funds with 5-7  banking days, and the funds aren't returned to your payroll account, contact Support.

In the meantime, you can cut a manual check in the amount of the net pay. Zenefits Payroll debits the employer/employee tax amounts from your payroll account when payroll is processed, so even if an employee's Direct Deposit transfer fails, the taxes that should be deposited for that paycheck are unaffected. 

If you're an employee, click here for more information

Why is this employee missing taxes in their paystub in Zenefits Payroll?

Zenefits Payroll relies on various information to determine the type and amount of taxes that an employee should have in each paycheck. There are four primary reasons why an employee might be missing a particular tax in their pay stub:

  • Wrong Home Address or Work Location: Zenefits Payroll uses the employee's work location and home address to determine which state taxes to withhold. If either address is inaccurate, Zenefits Payroll may not withhold the taxes you expect to see. See these instructions to update an employee's tax information in Zenefits Payroll.
  • Exemptions: Employees may be exempt from taxes for a number of reasons:
    • They provided a certain type of visa during onboarding, and may be exempt from paying FICA taxes.
    • They're a corporate officer (CEO, COO, President, etc.), and may be exempt from paying certain taxes.
    • They have one or more manually set exemptions. Learn more about setting exemptions in Zenefits Payroll.
  • Allowances and Filing Status: Employees who claim a sufficiently high number of allowances on their Federal or State W-4s may potentially have no withholding for either State or Federal income taxes. Try Paycheck City's paycheck calculator to determine whether an employee's number of allowances prevent income withholding.
  • Year-to-date Taxes: Employees who reach the Social Security wage base limit of $118,500 in a single calendar will cease to have Social Security taxes withheld for the rest of the year.

Am I required to collect unpaid taxes from employees?

In the event that an employee is undertaxed in a pay run, payroll administrators have two options:

  • Request that the employee reimburse the company for the taxes that were not withheld from that paycheck. In Zenefits Payroll, the tax amount can be recovered through garnishments.
  • "Forgive" the taxes. In this case, the amount that should have been paid as taxes is considered income to the employee. If this amount is greater than $600, you should issue a 1099 to the employee (much like you would for a contractor).

If you are using Zenefits Payroll and believe an employee was not taxed correctly, contact Zenefits Customer Care. 

How do I unsuspend Zenefits Payroll?

How do I unsuspend my payroll if I exceed my payroll processing threshold?

If Zenefits Payroll alerts you that your payroll is suspended because you've exceeded your company's payroll processing threshold (PPT), please contact Support immediately to resolve the suspension. Zenefits Payroll sets this PPT for companies who have 2-day payroll processing as part of its underwriting requirements, and won't initiate any ACH transactions until the suspension is lifted.

How do I upgrade from 4-day payroll processing to 2-day processing?

Please contact Support for more information about the current application process. 

Companies that have payments fail due to insufficient funds will be moved back a to 4-day processing schedule, unless they can provide a letter from their bank that claims fault for the funds not being present.

How do I cancel service with my previous provider?

To cancel service with your previous payroll provider, follows the steps listed below. Please note that this process is only for companies that switch payroll providers mid-year. 

  • Check if your old payroll provider has an online cancellation option. If you can't cancel online, you'll need to submit the following information to your previous payroll provider. Zenefits has created a form letter for this purpose here.
    • Ask them not to file your current quarter returns or annual returns for this calendar year. Zenefits will take care of these filings for you.
    • Ask them not to file your employees' W-2 forms for this calendar year, as Zenefits will also take care of these for you.
    • If you haven't done so already, request a refund for any tax refund payments that you've asked Zenefits to remit to tax agencies.
  • For your records, be sure to export and save, or request, all your quarter-to-date and year-to-date reports from your previous provider for this calendar year.
  • Finally, review your former provider's terms of service for information on any applicable cancellation fees, courtesy notice timelines, or billing refunds.
  • Zenefits cannot reach out to your prior provider on your behalf, please work with them directly on this process. 

If you are switching at the end of the year and will be running all payroll in the new year with Zenefits, then your previous provider can handle the taxes for the year you ran with them and Zenefits will take over filings for the new year. 

How do I run payroll in Zenefits?

To run your normal payroll, click onthe Payroll app, then Run Payroll Now to review and submit an upcoming run. 

Running your first payroll? Check out our instructional video first!

Here are step-by-step instructions for running regularly scheduled payroll:

  1. Select Run Payroll Now from the Overview page, or select Pay Runs, then click on the run you wish to submit in the Drafts table.
  2. On the Edit Pay Run page, you'll make changes to any pay details, if needed.
  3. Click Finish Edit to move to the final step.
  4. On the Run Summary page, you'll see:
    • Tax details 
    • The option to download the  payrun  in Excel 
    • The option to finish the pay run approval at a later time (please note that if the draft isn't approved by the deadline, this will result in a different check date)
  5. 5. Click Approve Run to process the run, and you'll be returned to the Pay Runs page with confirmation of a successful run via a green banner across the top of the page.

Here are step-by-step instructions for running an off cycle payroll:

  1. In the Payroll app, choose Pay Runs in the top menu bar.
  2. Click Add  Off-Cycle  Payroll  in the upper right corner of the Pay Runs page.
  3. You can either Create a new pay run or Clone an existing pay run
  4. Give the payroll a descriptive name, e.g., Christmas Bonus Payroll, and a pay date.
  5. Choose from the following options:
    • If this is for  Third-Party  Sick Pay, make sure to toggle this on
    • Include regular deductions & contributions: Health benefits that are normally deducted
    • Show a pay period on  paystubs: The dates the worker is being paid for use a  single-time  base tax withholding rate: Only select this if you want to withhold the employee at a different rate than they are usually taxed. If you do not select this at all, the employee will be taxed like normal, based on your company's pay schedule.
  6. From the list of available workers, check the box next to the names of each person who should be paid in the run.
  7. Click Edit Paystub on the right side of the screen to add earnings.
  8. After everything is entered, Finalize and Preview.
  9. Review the run and taxes, then Approve.

Manually Adding and Removing People in Zenefits Payroll

Administrators have the ability to choose whether someone will be added into or removed from future pay runs in Zenefits Payroll. These changes can be reversed at any time.

  1. Administrator goes to the Payroll app.
  2. Select the People tab.
  3. Select the individual's name and a detail window will pop over. 
  4. Select Add to Payroll or Remove from Payroll in the detail panel next to their name. 
  5. A pop-up will appear so you can confirm your request.

What is my Zenefits Payroll limit?

Zenefits Payroll does not give companies a specific set limit. Instead, the limit is dynamic and changes with your company. As a security measure, we don't disclose a dollar amount for your threshold, or list this amount in your account. This is to protect your company against possible loss.

If you do exceed the limit, your Zenefits account will be suspended and we will quickly reach out to you to notify you and provide instructions for next steps. There are no fees associated with suspension. 

If you have questions on a suspension, see this page for further instructions.

What is a Reverse Wire Drawdown?

What is a Reverse Wire? 

  • A new method for companies to fund their payroll runs. As the name suggests, a reverse wire is simply a wire that is initiated by the receiving bank rather than the sending bank. 

What are the benefits of funding payroll via reverse wire? 

  • It allows businesses to run payroll with a 2-day processing time if they do not qualify for 2-day ACH processing. 

Important information to consider prior to setting up reverse wire for your group: 

  • Your bank will likely charge you a fee for each Reverse Wire transaction. The fees vary from bank to bank and you can typically negotiate the rates with your bank. We recommend speaking to your bank representative to see what steps you can take to bring down the cost. 
  • All pay runs on a given check date are processed on one reverse wire. For example, if you have 3 pay runs for a single check date you will have one reverse wire processed  that covers both wages and taxes for all three runs.

How do I set up Reverse Wire to fund my Payroll? 

  • Reach out to our Customer Care team and let them know you are interested in setting up Reverse Wire for your group. They will loop you in with a member of the Banking Specialists team who will assist you with the set up!

How do I delete a pay run in Zenefits Payroll?

If you need to close out a pay run for any reason, you can do so by following these steps:

  1. Go to the Payroll app from your admin dashboard.
  2. Click into Pay Runs from the top navigation bar.
  3. Click on a pay run from the Drafts section.
    Note that you can only close runs that are in Draft status.
  4. Click on the three stacked dots on the upper right corner of the table.
  5. Click Delete Run, then Confirm.
    If you do not see the option to Delete Run, you'll need to wait until the pay period ends to close the run.

Please note that once you delete a run, it cannot be undeleted without assistance from Zenefits Support.

Calculating salaried workers' compensation per pay period

Zenefits Payroll makes the following calculations for your salaried workers in our system.


  Value Decimal Places Calculation Method 
Hours Per Year 2080 6 40 hours/week * 52 weeks = 2080, Industry Standard Value
Weekly Pay Periods (W) 52 6 Industry Standard Value
Bi-weekly Pay Periods (BW) 26 6 Industry Standard Value
Semi-Monthly Pay Periods (SM) 24 6 Industry Standard Value
Monthly Pay Periods (M) 12 6 Industry Standard Value
Weekly Pay Period Hours (W) 40 6 Hours per year/# of Weekly Pay periods
Bi-weekly Pay Period Hours (BW) 80 6 Hours per year/# of Bi-Weekly Pay periods
Semi-Monthly Pay Period Hours (SM) 86.666667 6 Hours per year/# of Semi-Monthly Pay periods
Monthly Pay Period Hours (M) 173.333333 6 Hours per year/# of Monthly Pay periods


Value Calculation Frequency
Pay Period Pay Salary/Pay Periods Calculate once
Salaried Workers Hourly Pay Rate Salary /2080 Calculate once
Gross Regular Pay Pay Period Pay - Sum of PTO Pay Per Pay Period
Regular Hours Pay Period Hours - PTO Hours Per Pay Period
PTO Hours From PTO or manually entered in edit pay stub Per Pay Period

Time Off

For salaried workers on semi monthly pay frequencies, calculating time off can cause questions. For example, if a worker takes 12 days of unpaid time off at the end of May, their pay might reflect as negative. Using the figures from the Constants and Calculations tables above:

86.666667 hours in a Semi Monthly Pay Period

12 days off * 8 hours per day = 96 total hours off in one pay period

The worker would see  -10 hours worked for that pay period.

When can I set check date to today?

If you are running an OFF-CYCLE:  
by CHECK... by CHECK...
If you are running a REGULAR pay run:  
by CHECK... by CHECK...

How will my staff know they've been paid?

Now, you can easily proactively notify your staff that it's pay day, all while you're approving payroll.

In the Approve Run step of running payroll, you'll notice a check box has been added that asks if you'd like to notify people via email and mobile app notification when the paystub becomes available.


If left checked, your staff will receive an email from Zenefits, as well as a mobile push notification on their phone if they have the Zenefits app downloaded, as soon as their paystub becomes available. This typically becomes available around 9:30am PST.

If you uncheck the box, no notifications will go out.

If you are paying by check, then no notifications will go out.

Since this cannot be disabled at an employee level, we recommend creating an off cycle run for any termination payrolls.

How to Set Up Reverse Wire in Zenefits Instructional Guide

To set up Reverse Wire for your company to fund payroll, please follow the three step process outlined below:

Step 1: Download the Reverse Wire Setup PDF.

  1. Log into your Zenefits Admin account.
  2. Click on the Payroll app.
  3. Select Settings.
  4. Scroll down to the Reverse Wire Settings section.
  5. Click the link: "Download additional information to assist with setting up reverse wire with your bank."

NOTE: If you do not see the Reverse Wire Settings section, please contact Customer Care or your Account Executive. They will work with our Banking team to enable these settings in your Zenefits account.

Step 2: Take the PDF to your Bank Relationship Manager and request to authorize Zenefits to initiate wire fund transfers.

  1. The PDF is for informational purposes only. Your bank should provide you with their own Reverse Wire Drawdown agreement form, as it can vary from bank to bank.
  2. This part of the process must be completed by an authorized signer on your account (Zenefits cannot set it up on your behalf).
  3. When you set your “Maximum Drawdown Amount,” ensure it's high enough to cover the combined total of pay runs you may process in a single day.
  4. Ensure the routing number you enter in Zenefits supports wire transfers (if it is only an ACH routing number, the transaction will fail).

Step 3: Once you have authorized Zenefits to initiate wire transfers at your financial institution, update your Reverse Wire Settings in Zenefits.

  1. Return to the Settings tab of the Payroll app in Zenefits.
  2. Click on the pencil icon to edit.
  3. Change “Zenefits has been authorized to initiate wire transactions for payroll purposes with [COMPANY NAME] bank” from No to Yes.
  4. Enter your Maximum withdrawal limit (USD).

After you complete the steps above, the Zenefits Banking team will change your company’s payroll drawdown type to reverse wire and you’ll be all set. If you have any questions, please don’t hesitate to reach out to our Customer Care team. We’ll be more than happy to answer any questions you or your financial institution may have!

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