FAQs About Running Payroll 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. 

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.

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.

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

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.

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.

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.

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.

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.

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):

However, the actual amount withdrawn to pay the run may be less, especially if some employees are paid by check.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

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:

The total cost is:

The total debit is:

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.

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.

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. 

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.

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).

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.

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

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. 

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!

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.

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.

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.

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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.