FAQ - Payroll Data Sync

The article provides a guide on frequently asked questions regarding syncing employee payroll data from BambooHR. It covers topics such as employee data management, handling deleted and terminated employees, and syncing for future hires. Employees can add their own information, and if a deleted employee is re-added, their records can be synced based on verified fields. Terminated employees remain in payroll until their final pay date, after which they are removed. Changes to their data post-termination will sync without payroll inclusion. The article also addresses scenarios like changing pay schedules mid-payroll run and syncing approved hours after payroll has started. Custom fields do not sync automatically, and data must be transferred to standard fields for integration.

  • Jun 10, 2026
  • Knowledge

Title
FAQ - Payroll Data Sync
Article Text
Payroll is included as an add-on.

What are the frequently asked questions when syncing data for payroll?

Purpose: This help guide will review frequently asked questions related to syncing employee payroll data from BambooHR.

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Table of Contents

Can I have my employees add their own information?

Yes! One of the best parts of BambooHR is that it allows your employees to help shoulder the responsibility of keeping data accurate. You can enable employee access to allow your employees to edit their own data. Also, check out this help guide to learn how you can allow your employees to make updates to their Pay Info tab. Now you can then focus on making sure the data is accurate rather than manually entering it.

Deleted employees

If an employee’s record is completely deleted from BambooHR, end dates will be applied to all records associated with the employee.

What if a deleted employee gets added back to BambooHR?

If an employee who was previously deleted gets added back to BambooHR and re-synced with Payroll, we will map the new BambooHR record to the previously created payroll record. We will verify the following fields to confirm that this is indeed the same employee: 

  1. Name
  2. SSN
  3. Date of Birth

Once linked, the sync will resume.

Future hires

If an employee's hire date comes after the end date of the pay cycle for which payroll is being processed (either scheduled or manually), we will not sync the employee(s) data for payroll.

Terminated employees

Terminated employees will continue to be included in the payroll until their final pay date. Once their final pay date has passed and they have been paid for the last time, we will remove them from the payroll. 

If changes occur in the demographic data for terminated employees after the final pay date, those data changes will automatically sync to BambooHR Payroll without including the terminated employees in payroll. Employees must have the Terminated employment status on their Job tab to ensure they are made inactive in the system and that all employee data is up-to-date for tax reporting.

What if I mark an employee as inactive in BambooHR?

If an employee’s record gets moved to ‘Inactive’ in BambooHR, we will immediately stop syncing that record to Payroll. If you need the employee to continue syncing with Payroll, you will need to set them to an active or terminated status.

If the employee is later reactivated, we will resume the sync of their data to Payroll.

What if I rehire an employee?

If a terminated employee is rehired in BambooHR, we will ensure that their final pay date gets removed, that they get included in payroll again, and that we resume syncing that employee's information for payroll.

What if I switch an employee's pay schedule mid-payroll run?

Every time you navigate to the Payroll Center, we will be performing a behind-the-scenes check to ensure that we’ve got employees assigned to the correct pay schedules on the payroll side. If for some reason any of your employees has moved between pay schedules, and the pay schedule they were previously in has an open payroll, we will cause an error message to appear when you open the payroll informing you that you either need to remove the employee from the open payroll or reset the payroll entirely.

What if the employee is removed from a syncing pay schedule?

If an employee is completely removed from a syncing pay schedule or moved to a pay schedule that doesn’t sync with payroll, we will stop syncing their data to Payroll.

Will any of my custom fields sync to payroll?

Custom tables and fields, such as direct deposit, federal withholding, and state withholding fields that our BambooHR Support team has added to your account are not part of the payroll integration. You must have this data transferred to the standard fields that are on the Pay Info tab. 

If you transfer payroll data from custom tables to the standard fields on the Pay Info tab, please contact the BambooHR Support team once you finish, and they can help you remove the custom fields and tables to avoid confusion and double entry.

How do I sync approved hours after payroll has been started?

If you adjust and approve an employee's time off hours after you start payroll, you can sync this data by resetting the payroll run. Navigate to the Edit page of the payroll run, click the three-dot menu at the top right, and select Reset. Keep in mind that resetting the payroll will remove any edits previously made to the payroll. For more information on how time off hours sync to payroll Time off hours, click here! 

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