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FAQs About Using Zenefits Payroll

How do I add deductions to Zenefits payroll?

Deductions for any benefits managed by Zenefits are automatically added to Zenefits Payroll. To add deductions for benefits managed outside of Zenefits to a Zenefits Payroll account, see this guide to adding deductions and contributions to Zenefits Payroll.

Follow these instructions to add garnishments in Zenefits Payroll, and keep the following in mind:

  • If you'd like to add a garnishment for a specific number of paychecks, see here
  • If you'd like to add a recurring garnishment, see here.  

What's the difference between a paystub and a pay template?

In Zenefits Payroll, an employee's pay template determines the recurring earnings, deductions, and contributions that they'll have in each pay run. Changes made to a pay template are effective in the next run, and will show up in all future runs.

An employee's paystub lists the details for earnings, deductions, and contributions in a single run. Changes made to an employee's paystub will override their pay template and show up once, in the next run. After that, the employee's earnings, deductions and contributions will revert to the values in the pay template.

Where can I find my staff's paystubs in Zenefits payroll?

If you're an administrator for a company that uses Zenefits Payroll, you can view historical paystubs for each worker, and download each paystub as a PDF. Paystubs for both active and terminated individuals can be accessed the same way. 

  • Choose People from the Zenefits Payroll app.
  • Select the person you wish to see more details about.
  • Choose Paystubs to view the most recent paystub, or select a historical paystub from the list.

Workers can download their own paystubs in their Paystub app on their dashboard.

How do I know when I've been paid?

No more wondering if it's pay day-- Zenefits Payroll notifies you through the app when you're paid! If you have the Zenefits app on your mobile device, you'll get a push notification on your pay date. Tap on the push notification to be taken straight to your pay stub.

I don't like notifications, can I turn these off?

Absolutely. If you've turned notifications on in the past but would like to turn them off moving forward, you can follow the directions below. If you've previously disabled notifications, then you won't receive pay day notifications.

  1. Open the Zenefits app on your phone.
  2. Tap on More in the bottom menu.
  3. Tap Settings.
  4. Tap Open iOS Settings then Don't Allow in Notifications.

How can I change the company bank account used by Zenefits Payroll?

You can update the bank account used to fund your Zenefits Payroll pay runs in your Company Profile app. 

Go to the Payroll Bank Account section of the Billing & Payments tab and click Change. 

You will then see a pop-up message with more information about the processing time for the change. 

Please start this process at least 7 business days prior to your next payroll processing date. 

If you have a supported bank, you can use the Instant Verification. If your bank is not supported or if you do not want to provide the required information, you can select Manual Verification

Follow the prompts to complete the process for your selected verification type.  As a reminder, be sure you have the proper funding available before approving a pay run. 

 How do I run reports in Zenefits Payroll?

Run payroll reports by selecting from the following available reports:

Heads up: Some payroll reports will be emailed to you instead of immediately downloaded.

  • All-in-One: Includes all historical runs, with employee earnings, deductions, contributions, and taxes in each run.
  • Bank Transactions: Lists bank transactions using the payroll account, e.g., payments to employees.
  • Bank Transactions Details: Aggregates all payroll related credits and debits processed by Zenefits in one place, including detail for federal, state, and local transactions.
  • Payroll Summary Report: This report records the financial impact of each payroll on a client company and allows clients to make informed decisions on  payruns  and funding. Additionally, it gives subtotals and totals for a client's payroll run (or custom period) for each individual earning, deduction, garnishment, contribution, employee tax, employer tax, and totals for each category.
  • Payroll Register Report: This report allows clients to see a summary view of total earnings, deductions, contributions, taxes, and total cost at the check level for a selected payroll run or alternatively, all payroll runs over a selected period.
  • Labor Distribution Report: This report allows clients to see an accounting statement that details hours worked, wages earned, and other summary data by department and/or location.
  • Payroll Detail Report: This report allows administrators to see summary information of paychecks by employee to allow informed decisions in reviewing payroll. It also gives detail on the run (or period) by employee check on all earnings, deductions, garnishments, contributions, employee taxes, and employer taxes. It can be sorted and subtotaled by location and/or department, and by name. Additionally, the report provides employee details, including SSN, hire date, location, department, address, period, check date, etc.
  • Employee Detail Report: This report allows clients to see all the information that's currently in payroll for each employee--that  includes new, ongoing, and terminated employees. It also allows clients to view their withholding allowances, filing statuses, and personal information.
  • History Summary Report: Provides a summary view of all earnings, deductions, contributions, and taxes per year and by all quarters, for individual employees or company totals. It includes earnings, deductions, garnishments, contributions, employee taxes, employer taxes, and totals for every quarter & year to date for each category.
  • Wage and Tax Summary Report: Allows clients to see gross wages, taxable wages, and taxes that are subject to federal, state, and local withholdings. It captures each employee's tax setup, including:
    • SSN (masked)
    • Federal, work & residential state status & allowances (and local taxes if applicable)
    • Gross wages
    • Each employee tax & employer tax (including taxable wages & total taxes)
    • This report can be run for any period, sort, and subtotal by Department or Location
  • Tax Liability Report: This report allows clients to see a detailed breakdown of all Payroll Tax Liabilities for a pay period. The report can be sorted and subtotaled by federal, state, and localities within states. For any selected period, this report captures:
    • Individual employee taxes
    • Individual employer taxes (including total liability for each)
    • Prepaid or client responsibility amounts
    • Zenefits deposited & pending amounts

Administrators can select a group of employees by department, location, and other categories. Admins can also select for all employees to get individual reports for each employee in the group. A company level report can be run for totals for each item and category.

  • Garnishment Setup: This report shows each employee that has a garnishment in place, as well as their set up date, SSN, garnishment details, and status.
  • Garnishment Audit Report: This report captures garnishment data, sorted by employee, check date, amount withheld, any uncollected administrative fee, and the amount to submit to the agency or  3rd party.
  • Workers Compensation Calculation: This report will display all the liabilities you need to determine if your company is subject to Workers Compensation requirements.
  • W-2  Preview : The  W-2  preview will help you ensure a smooth year end processing. Please review and verify that the information appears to be correct.

If you'd like to run a report to reconcile payroll, you can run the  All-in-One  report for that payroll's check date.

How do I manage departments in Zenefits Payroll?

Zenefits Payroll uses the same HR departments as the rest of Zenefits. Workers can be assigned to multiple departments.

  • Managers and administrators can request a change to departments by opening the Employee Tearsheet. You can access this by clicking the Show Details link next to someone's name in the People tab of the Payroll app, then clicking the Open  Tearsheet symbol Screen_Shot_2018-12-28_at_2.18.20_PM.width-800.png on the Details tab.
  • Administrators can also create and edit departments in Zenefits.

Reconciling Payroll

Learn how to reconcile payroll.

Payroll reconciliation is the process of comparing your internal accounting records (such as a company bank statement) against your pay run(s) to ensure accuracy. Reconciling will help to identify possible account errors or mismatches caused by possible credit(s) applied to payrun( s ) and/or the Level of Service of your Taxes.

To reconcile the amounts that Zenefits Payroll debited for the taxes and worker net pay (by Direct Deposit) in a particular payroll, the following reports payroll administrators can run to reconcile payroll: 

  • All-in-One Report: Run the All-in-One  Report and enter the payroll's check date for the report's Start and End date. 
  • Bank Transaction Detail Report: This report will break down the following pay types and will reflect the amount that Zenefits Payroll will debit form your company’s payroll account: 
    • Net pay & any reimbursements for all workers paid by Direct Deposit 
    • All worker and employer taxes set to full service 
  • Payroll Summary: This report reflects the totals for gross pay, net pay, total taxes and employee taxes by jurisdiction, and deductions and contribution totals (by type).  

Note: The debit amount reflected on the bank transaction detail report excludes any net pay for workers who are paid by check, and all deductions or contributions for ?workers'? benefits . Zenefits will also pull this amount in two separate debits: one for worker pay and one for all related payroll taxes that are set to full service.

Can I use Zenefits Payroll with my accounting software?

Yes! You can set up Zenefits Payroll to automatically sync pay run information to QuickBooks Online and Xero, or export payroll report files and upload them to QuickBooks Desktop.

Can I export IIF files from Zenefits to Quickbooks?

You can set up Zenefits Payroll to export payroll information using Inuit's IIF file format and upload these files to QuickBooks Desktop. Learn more.

IIF file export is not available for companies that do not have Zenefits Payroll.

How do I cancel Zenefits Payroll?

If you are actively using Zenefits Payroll and would like to discontinue use, please contact Zenefits Customer Care for assistance.

If you need to cancel a direct deposit, cancel an entire pay run, or paid an employee the incorrect amount and need it corrected, please contact Support for further assistance.

You may also find more information about pay run reversals here.

How do I manage an employee on a leave of absence in Zenefits payroll?

Zenefits Payroll currently does not have functionality to automatically remove or add employees on leave of absence. In the meantime, you'll need to manually uncheck any employees on LOA in each run before you run payroll.

  • For any period in which the employee isn't working at all, make sure to remove the employee from the run by click the checked box next to their name. If you see a line through their name, they won't be paid in the run.
  • For any period in which the employee works only part of the period, uncheck them from the regular run, then run an off-cycle payroll, and add the employee by click the empty box next to their name. Then, add prorate their pay for that period and add it as Regular Earnings.

Here's how to prorate a salaried employee's paycheck. For hourly employees, just enter the number of hours worked.

Note that removing an employee from a run from doesn't affect future runs, so you'll need to do this each time you run payroll while the employee is still on LOA.

For more information on removing employees when running payroll, see this guide to running off-cycle payroll in Zenefits Payroll.

Why am I being terminated from Zenefits payroll?

Before your company's account with Zenefits Payroll is terminated, you'll receive multiple messages regarding why and how the termination will take place. There are three reasons you may be terminated from Zenefits Payroll:

  1. You stopped running payroll with us.
    If we notice a long lapse without your company processing a pay run, we'll reach out and ask if you would like to cancel your account. Eventually, we will terminate your account for you.
  2. Your company has gone out of business.
    If your company goes out of business, we will terminate your account.
  3. You have decided to leave Zenefits Payroll.
    If for any reason you choose to leave Zenefits Payroll, we will terminate your account.

Why are there hours showing on my salaried employee's paystub?

Zenefits Payroll will automatically show hours on the pay stub for all employees. The hours are automatically generated and are not intended to reflect actual hours worked. It is an automatic calculation based on assumed 8 hour work days. 

Here is a breakdown of how the calculation works: 

There are 40 hours in a work week and 52 weeks in the year. 

40*52= 2080 hours worked in a year 

  • For semi-monthly pay frequencies, there are 24 pay periods for the year. 
    2080/24 = 86.67 hours per pay period
  • For bi-weekly pay frequencies, there are 26 pay periods for the year.
    2080/26 = 80 hours per pay period

If there is a holiday or Time Off request, the automatic calculation will account for this and subtract the hours so it shows hours worked based on a per day proration. 

2019 Annual Changes  
  2019 2018
Social Security Wage Base $132,900 $128,400
Employee Social Security Tax Rate 6 .20% 6 .20%
Medicare Wage Base None None
Medicare Tax Rate 1 .45% 1 .45%
Additional Medicare Tax Rate on earnings in excess of $200, 000 0.9% 0.9%
Maximum Limitation for annual benefit under §415( b )( 1 )( A ) for defined benefit plans $225, 000 $220, 000
Maximum Contribution Limitation for defined contribution plans under §415( c )( 1 )( A ) $56, 000 $55, 000
§402( g )( 1 ) (applies to §401(k), and §408( k )( 6 ) salary reduction SEPs) $19, 000 $18,500
§403( b ); non-profit employers; taxsheltered annuities $19, 000 $18,500
§457; state & local governments; tax exempts $19, 000 $18,500
§408( p ); SIMPLE IRA plans $13, 000 $ 12 ,500
§401(k), §403( b ), §457, SEP Catch-up $ 6 ,000 $ 6 ,000
SIMPLE Catch-up $ 3 ,000 $ 3 ,000
Medical FSA Limit $ 2 ,700 $ 2 ,650
Business Mileage Rate $ 0 .58/ mile $ 0 .545/ mile
Charitable Activity Mileage Rate $ 0 .14/ mile $ 0 .14/ mile
Relocation Related Mileage Rate* $ 0 .20/ mile * $ 0 .18/ mile *
Medical Related Mileage Rate $ 0 .20/ mile $ 0 .18/ mile
Commuter Highway Vehicle Fringe Benefit Limits $265/ month $260/ month
Transit Pass Qualified Fringe Benefit Limits $265/ month $260/ month
Qualified Parking Qualified Fringe Benefit Limits $265/ month $260/ month
Personal Use of a Company Vehicle Cents/Mile Rate $ 0 .58/ mile $ 0 .545/ mile
Employer-Provided Adoption Assistance Dollar Limitation $14,080 $13,810
Qualified Small Employer HRA (Individual Family) $ 5 ,150 $ 5 ,050
Qualified Small Employer HRA (Individual Family) $10,450 $10,250

*Military only

Tips to avoid Payroll and Tax corrections

Learn about the different tips to avoid payroll and tax corrections.

To help you understand Zenefits Payroll, we ’ve put together key information containing important payroll and tax tips.


During your Zenefits journey, it is important to ensure your tax information is up to date. Below are some common mistakes and how to avoid them: 

  • Incorrect tax rate in SUTA Accounts: New rates are typically sent out at the end of November through December. As those new rates are provided, administrators should update/confirm their rates for the new year. 
  • Incorrect tax deposit schedule within tax cards: Tax deposit schedules can change as a company grows. Companies will receive notices by mail or portal for a change in deposit schedules. Typically, this happens at the beginning of the year but could change at any time a company meets monthly filing or payment requirements. Administrators should update their tax deposit schedule as soon as a notice is received. 
  • Incorrect number (or format) in tax cards: Utilizing the State Payroll Tax & Registration Guides provides information to administrators on correct formatting of state tax jurisdictions. 
  • Employees assigned to incorrect work locations: The accuracy of an employee’s home and work location is essential to accurate tax filings. Wrongly allocating employees to avoid new state set-ups, or to postpone set-up for a new tax jurisdiction result in inaccurate filings and costly corrections. View the Zeneskills training on Work locations and their effect on payroll 
  • Calculate Only vs Full-Service: Zenefits offers two levels of service when it comes to your taxes, and it is important to understand the differences between the two. 
  • Calculate Only: Zenefits will calculate any employee/employer taxes related to a jurisdiction and display this amount in your quarterly tax package. Zenefits will not withdraw funds for the calculated taxes, remit the calculated tax amounts, file tax returns, or resolve notices for the respective tax agency. Companies are responsible for tax payments while pending full-service. Once they receive confirmation, they are full-service, Zenefits will begin to debit for taxes. Payruns will have two debits: one for wages and secondary for tax.  
  • Full-Service: Once a company is in full-service, Zenefits will calculate, collect, remit and file taxes for the appropriate jurisdictions. Company administrators should ensure accurate rates, filing frequency, and account numbers are updated as needed. 
  • Managing Benefits Costs for S-Corp Owners: One of the most common end of year corrections on W-2s is when S Corp shareholders who own more than 2% have not allocated their benefit contributions as income. These shareholders must have their benefits taxed and therefore will need their own pay type. If an S-Corp with 2% or more shareholders need guidance they can utilize the help center article linked or reach out to the Zenefits tax team, Advisory Services (if included on their account), or their internal tax advisor. 

Handling Payroll and Tax issues

Learn how to handle payroll and tax issues.

The following information will assist administrators on how to handle some of the more uncommon payroll and tax issues. These videos walk through these items in more detail. Please note, most of these items have extra fees. Please reach out to customer care if you need assistance on any of these items. 


When an employee states it is past the paydate and they haven’t received their check. 


A method for companies to fund payroll. A reverse wire is initiated by the receiving bank rather than the sending bank. This allows businesses to run payroll with a 2-day processing time.  


If you miss your company approval deadline for payroll, your check date will automatically move to the next day. If Zenefits is notified timely, the check date may be moved back to the original date. 


If your company receives a tax notice, this video will review how you can potentially resolve yourself and the steps you can take to avoid getting notices. 


A debit failure happens if Zenefits is unable to obtain the funds required to process your current payrun. 


A stop payment is when you attempt to stop a payment from being deposited to an employee’s bank account. 


A payroll reversal is the process of sending a request to a receiving bank to reverse and original direct deposit payment. 


A 1099 correction could be needed if a company doesn’ t opt into Zenefits filing the 1099 on their behalf or if payments were incorrect or made outside of payroll. 


A payroll correction may be needed if adjustment or correction needs to be made to an already paid out pay run for a prior quarter. Administrators can adjust previous pay runs (within the same quarter) by following these steps


A tax setting correction is when a correction is needed to deposit schedules, tax rates and EIN information. 


A form W-2 correction may be needed after W-2’ s are issued. Corrections can be related to SSN, earnings, work and home locations, pay types and deductions. 


This type of payroll correction if inaccurate information was uploaded during implementation or after implementation was completed. 


A tax filing amendment is needed to correct a past filing due to incorrect earning amounts, work locations, home addresses, pay rates, and deductions. 

Payroll Tips

Learn about the different tips for payroll.

The following payroll training will assist payroll administrators on how to reconcile payroll to ensure accuracy and reduce the need to corrections. 


The all-in-one report lists all earnings, deductions, contributions and taxes by payroll run for the selected period. 


The payroll detail report shows detailed payroll activity for employees including earnings, taxes, deductions and employer liabilities. 


The W-2 preview will help you ensure a smooth year end processing. Admins can review and verify that the information is correct for their employees W-2s. 


Allows payroll administrators to view changes that affect upcoming and past payrolls. 


Review different pay type categories and how it impacts taxable earnings. 


Review how an employees work location vs home address impacts taxation.  


Review how to setup tax withholding exempt status for employees. 


Review how the taxation of bonuses affects your employees’ pay. 


Review how an employee’s leave of absence affects payroll. 


Review how overtime exempt status affects pay schedules and pay runs. 


Review how an employee termination affects payroll and how to manage final pay. 

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