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FAQ about Zenefits Payroll Accounting Integrations

How can I map my chart of accounts?

You will be able to map the Zenefits Payroll transactions to your accounting chart of accounts in the Settings tab of the Payroll app. If this is your first time setting up the sync, in the Organization tab from the left-hand menu, you will see the option to add accounting software by clicking on the orange Sync button. 

After the sync is set up, you can click Edit to map the transaction types. It will look something like this: 


To properly export the information, every transaction type MUST have an associated account. Even if you are not using the transaction type now, the mapping must be completed for the export to work correctly. 

What are the general guidelines for completing the chart of accounts mapping?

In order to ensure your Zenefits Payroll information is exported to your accounting software correctly, you should follow these general guidelines: 

  • All Earnings (including  S Corp) & Reimbursements = Expense account
  • All Deductions = Liability account
  • All Garnishments = Liability account - at this time Zenefits Payroll does not make payments to Garnishors so these are deducted from employee pay and then the company is required to manually pay the appropriate agency 
  • All Employer Taxes = Expense account
  • All Employee Taxes (For either Checks and Direct Deposit) = need to be mapped to a Liability or for QuickBooks Online it could be mapped to "Cash" e.g. Company Payroll Account based on how your reconciliation is done. 
  • All Employer Contributions (401( k ), Medical, Dental, Vision, etc.)  = Expense account
    • Please note the total cost for benefits will not automatically export to your accounting software. You should manually enter these amounts as you receive your invoices. 
    • Generally, it is best to enter the carrier invoice cost at the beginning of every month. Because the employer portion of benefits is not associated with any money movement in payroll, Zenefits has decided to have clients manage this outside of the accounting export from payroll processing. 

If the mapping is not set up using these guidelines the accounting export will not work correctly. 

How long will it take for my Zenefits Payroll pay run to export to my accounting software?

If you have selected to automatically export your payroll information into your accounting software, it may take up to 24 hours from the check date to complete an export. 

To edit your accounting sync settings, click Edit in the Organization tab of the Settings section of the Payroll app. You will see an option that looks like this: 


The automatic sync option is NOT available for QuickBooks desktop. 

I've updated my accounting integration mapping, how can I export my pay runs?

After you update your accounting integration mapping, all future runs will be exported using your new set up. If you would like to update past pay runs to reflect your new mapping, you will need to manually export them.

If you are updating past runs, be sure to first delete the export file with the incorrect mapping from your accounting software. You can then go to the Payroll app on your Zenefits dashboard and click on the Pay Runs tab. Click on the pay run you need to correct and at the bottom of the payroll information on the left-hand side you will see the option to Export. This will generate a new file to be exported to your accounting software. If you have the automatic sync, it will be automatically sent. If you have the manual option a file will download for you to add to your accounting software. 

How can I use Quickbooks Online with Zenefits payroll?

You can set up Zenefits Payroll to automatically export pay run reports to QuickBooks Online, or you can choose to manually export each run when you submit it.

  1. Sync the QuickBooks account with Zenefits Payroll by following these steps.
  2. When a payroll run is processed for payment, and shows up in the Completed - Paid Runs table, the run can be automatically or manually exported to QuickBooks.
  3. Then you'll log in to your  QuickBooks account, and approve the transactions in the run.
  4. After you approve the latest transactions, Quickbooks will take care of bank reconciliation for you.
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