Completing the Zenefits Payroll Application

To complete the payroll application, you will need to provide the following:

  • Company Business Information
    • Company Name
    • Trade Name/Doing Business As (if applicable)
    • Legal Name
    • NAICS Code

  • Employee Information
    • Full Name
    • Title
    • Email Address
    • Hire Date
    • Employment Type
    • Work Address
    • Compensation Type and Rate

  • Company Ownership Details
  • Company Signatory
    • First Name
    • Last Name
    • Title

  • Company Banking Information
    • Routing Number and Account Number, OR Business Checking Account
    • Voided business check (to verify that your business account is not also for personal use)

  • Desired Start Date Please note that after we have collected the documents, implementation can take up to 30 days, but this can vary based on the size of the company, packages purchased, and your availability. 
1. Company administrators can start the application by clicking on the Payroll app on their dashboard and selecting Get Started.

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2. Answer the questions that appear, including:
  • Whether you've paid employees in the current year
  • Who your current payroll provider is (if applicable)
  • Whether your employees receive either cash tips or pay for clergy
3. Click Enroll Now.
4. Next, you’ll be taken to an overview of the steps for completing the application. Each time a section is completed, you will be brought back to this page to see your progress. PYP App Guide Image 2.png
5. Click Start and enter the Company Name, Trade Name/Doing Business As (if applicable), Legal Name, and NAICS Code. Then, click Next. PYP App Guide Image 3.png
6. You’ll be brought back to the overview page. Click Continue to start adding employees to payroll.
7. Select Add Employee and enter the employee’s information you're prompted to provide. When you're done, click Save.
  • You will need to add at least one employee in order to complete the application. Repeat step 7 to add all of your employees, or if you prefer, upload them in bulk later in the application process.
8. Select Continue to designate your company’s signatory for payroll. You can select either yourself or another employee of the company. Enter the requested information for the signatory, then click Continue. PYP App Guide Image 4.png
9. You’ll be brought back to the overview page. Click Continue to verify your bank account.
10. Select Begin Verification.
11. Choose how you want to verify your bank account and select Continue. PYP App Guide Image 5.png
12. Follow the prompts for verifying your bank account.
  • If you select Instant Verification, you will need to provide your username and password for your bank.
  • If you select Manual Verification, you will need to provide the routing and account number. Once you've received test deposits from Zenefits Payroll in the bank account you've provided, enter the amounts that Zenefits Payroll deposited within the Billing & Payments section of the Company Profile to verify your account.
13. Upload a voided business check and select Submit.
14. You’ ll be brought back to the overview page. Click Continue to enter your desired start date.
15. Select your desired start date and then click Save & Continue.
16. You’ll be brought back to the overview page. Click Continue to complete the application and review next steps.

Officers will need to be listed as an employee within Zenefits in order to complete the application. When completing their information, you can enter their salary as $0.01. You are able to add them temporarily and delete the employee profile once the application is complete, however, we recommend leaving them listed as an employee in Zenefits for your company's Organization Chart. You are able to mark the employee profile as 'Not on Payroll' so they don't show up in your pay runs as well.

1. Once you have completed the payroll application, you will see a list of tasks on the Overview page of the Payroll app.
2. Click on the down arrow to expand the Upload Payroll Documents task and select Upload Documents.
3. Upload the required payroll documents under the appropriate section and then click Submit for Review.

For more information on what documents are required, check out Zenefits Payroll Setup Checklist in the Help Center.

4. Click Okay in the dialog box, and then select the Overview tab to be brought back to the main page.
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5. Click on the down arrow to expand the Verify Your Bank Account task.
  • If you elected Instant Verification during the application, this task will be marked as complete.
  • If you elected Manual Verification, click Verify Account.
6. You will be brought to the Billing & Payments section of the Company Profile. Enter the amounts of the two test deposits from Zenefits Payroll under the Payroll Bank Account subsection and click Verify.

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7. Click on the three horizontal lines in the top left corner to open the navigation sidebar and select Payroll. This will bring you back to the Payroll app.

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8. Click on the down arrow to expand the Upload a Voided Check task.
  • If you uploaded a voided check during the application, this task will be marked as complete.
  • If you selected I’ll do this later during the payroll application, click Upload Check.
9. You will be brought to the Billing & Payments section of the Company Profile. Upload a voided business check within the Payroll Bank Account section.
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10. Once your Implementation Manager has reviewed and approved your payroll documents, navigate back to the Payroll app.
11. Click on the down arrow to expand the Update and Confirm Employee Info task and select Get Started.
12. Select +Add Current Employee, enter the employee’s information in the dialog box and click Invite Employee to Zenefits.
13. Next, navigate to the Terminated tab. Here you will need to add any former employees who were paid in the current fiscal year.
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14. Select +Add Former Employee, enter the employee’s information in the dialog box and click Save.
15. Once all employees who are working or has worked for you this year are listed in the table, click Yes, All My Employees Are Listed Above.
16. Click on the down arrow to expand the Set Up Your Tax Information task and select Get Started.
17. You will be brought to the Taxes section of the Settings page.
  • Please note that this page will automatically populate the required jurisdictions based on the states where you have employees working and/or living.

18. Click on the pencil icon in the top right corner of the federal or state tax information box.

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19. Enter the tax information for the jurisdiction and click Save.
20. Once the tax information has been entered for each jurisdiction, click Tax Setup is Complete.

For more information check out our Help Center pages on the Zenefits Payroll Setup Checklist , or registering with individual state payroll agencies .

21. If you are the assigned payroll signatory, click on the down arrow to expand the Sign All Documents task and select Get Started.
22. You will be brought to the Reports & Forms page.
  • Please note that this page will automatically populate the required payroll documents based on the states where you have employees working and/or living.
23. Click the Sign Form button. This will open a dialog box allowing you to electronically sign the payroll document.

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24. Provide your electronic signature within the signature box.
  • If you have trouble with this, use your mouse to click and then hold down on the mouse while dragging it in the gray box to create/draw your signature.

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25. Enter your full name in the bottom box and then click Sign.
26. Once all payroll documents have been signed, click All My Forms Have Been Signed.
27. Click on the down arrow to expand the Set Up Pay Types task and select Get Started.
28. Review the Pay Types that have already been added, if there are any other pay types that have been used in the current fiscal year, click +Add in the appropriate section.
  • Be sure to review and set up pay types carefully as these are used to calculate paychecks and process payroll.
29. Enter the pay type information with the dialog box and click Create.
30. Once all the Pay Types have been set up, click All My Pay Types Are Set Up.

The tax jurisdictions will be listed as Calculate Only by default. Once you have entered the account details for all the jurisdictions, Zenefits will establish the Full-Service integration. You can expect to have your Levels of Service updated by, or shortly after, your first pay run. 

If tax jurisdiction account numbers are provided within the current quarter, the effective date can be backdated to accommodate Zenefits debiting, remitting, and filing for this agency on your behalf.

Please note that if you wish to change your level of service for any tax jurisdictions after implementation has been completed, you'll need to contact Zenefits Customer Care to get the process completed.

In order to sign the payroll documents, you will first need to complete the Update and Confirm Employee Info and Set Up Your Tax Information tasks.  

In order to sign the payroll documents, you must be the assigned payroll signatory. If you are the payroll signatory, you will see a Sign Your Company’s Payroll Documents To Run Zenefits Payroll task at the top of your dashboard. If you do not see this task but you are the signatory, you may need to log out of your admin dashboard and log into your employee dashboard.

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If any changes are made to the employee roster within the Update and Confirm Employee Info task (i/e: an active or terminated employee is added, or an employee’s information is changed), this may update the required tax jurisdictions. In this case, you will need to complete the Set Up Your Tax Information task and sign the payroll documents again.

To update worker information:

1. Click on the People tab within the Payroll app
2. Click Show Details next to someone's name, then Details and this icon ee tearsheet be taken to their tearsheet
3. Select the pencil icon to edit the section.
4. Select Save to confirm the changes.
  • Please note that some changes to demographic information may update the required tax jurisdictions. In this case, you will need to complete the Set Up Your Tax Information task and sign the payroll documents again.


To add a current or former worker:

1. Click on the People tab within the Payroll app.
People Tab
  • To add a current employee, select +Add Current Employee, enter the employee’s information in the dialog box and click Invite Employee to Zenefits.
  • To add a former employee, click on the Terminated tab and select +Add Former Employee. Then enter the employee’s information in the dialog box and click Save.

2. Once all your current employees and your former employees terminated this year are listed in the table, click Yes, All My Employees Are Listed Above.
  • Please note that some changes to employee demographic information may update the required tax jurisdictions. In this case, you will need to complete the Set Up Your Tax Information task and sign the payroll documents again.


To update tax information:

1. Click on the Settings tab within the Payroll app and then select Taxes from the left menu bar.
Payroll Taxes

  • Please note that this page will automatically populate the required jurisdictions based on the states where you have employees working and/or living.

2. Click on the pencil icon in the top right corner of the federal or state tax information box.
3. Enter the tax information for the jurisdiction and click Save.
4. Once the tax information has been entered for each jurisdiction, click Tax Setup is Complete.


To upload additional payroll documents:

1. Click on the Settings tab within the Payroll app and then select Implementation Documents from the left menu bar.
IMP Dox
2. Upload the required payroll documents under the appropriate section and then click Submit for Review.


To update pay types:

1. Click on the Settings tab within the Payroll app and then select Pay Types from the left menu bar.
Pay Types
2. Click +Add in either the Earnings, Deductions, or Contributions section.
3. Enter the pay type information with the dialog box and click Create.
  • Be sure to set up and review pay types carefully as these are used to calculate paychecks and process payroll.

4. Once all the Pay Types have been set up, click All My Pay Types Are Set Up.

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