Changes to Benefits with BambooHR® Payroll


Purpose: To help you understand how BambooHR® Payroll integrates with the benefits module (either Benefits Tracking or Benefits Administration) in BambooHR and what benefit settings automatically sync to Payroll.
- Help Guide: For comprehensive understanding of setting up benefit plans, we recommend reviewing the Benefit Plans help guide details as you read through this guide on Payroll-specific settings.
- BambooHR® Learning Course: Did you know we have a course that will walk you through setting up benefits with Payroll? Click here to learn more!
Benefit settings synced to Payroll
When using BambooHR® Payroll, only certain benefits-related settings will automatically sync to Payroll.
Syncing benefit plan setup data
Benefit plan type | This pertains to what benefit plan type you have selected from the +Add Plan dropdown menu on the Benefits tab. |
Plan type | Some benefit plan types have additional plan types to select from. This is found in the Plan Details step of the benefit plan. |
Pre-tax/post-tax setting | This setting found in the Payroll Deduction step determines the deduction type that should sync to Payroll. In turn, the deduction type will determine how the deduction will be taxed and is shown in Payroll and on the employee’s paystub. |
Safe Harbor-matching contribution | If this setting is enabled in the Eligibility (and Cost) step of the benefit plan setup, the contribution amounts will automatically adjust to Safe Harbor rules during each payroll run. |
The start and end dates of a benefit plan do not sync to Payroll. However, the dates for the employee’s benefit deductions will sync to Payroll, according to their benefit enrollments.
For more information on what benefit/non-benefit deduction fields sync to Payroll, click here!
Benefit plan setup

If you already have your benefit plans set up in BambooHR, you will see a migration modal when first navigating to Benefits settings after having the payroll integration enabled. You will need to go through and determine the deduction schedule for each benefit plan type.
Plan details
In the Plan Details step, the Plan Type field requires a selection for the following benefit plan types. Options will vary based on the benefit plan type:
- Retirement
- Supplemental Health
- Flex Spending Account (FSA)
- Disability
- Other
The Plan Type field will not be editable if the plan has at least one current or scheduled enrollment.
Eligibility and cost
Some plans, typically variable rate plans, will show this step named as "Eligibility" without cost specifications, and you will need to determine costs for each employee's benefit enrollment.
When entering costs for employees included in Payroll, any employees with an assigned pay schedule that syncs with Payroll are required to have monthly costs listed in USD. If the plan uses another currency, it will not appear as an option in the Benefits Overview table for those employees.
If you are setting up a 401(k), Roth 401(k), or 401(k) After Tax retirement plan, you will also have the option to enable a Safe Harbor matching contribution for the plan. If enabled, the contribution amounts will automatically adjust to Safe Harbor rules during each payroll run. Please note that this setting will apply to all current and future 401(k) and 401(k) Roth plans and automatically update those plans’ settings. You must reset your payroll for these changes to reflect on an open payroll run.
Payroll deduction
When using Payroll, the following fields will appear in addition to the standard fields in the Payroll Deduction step:
-
Is the Payroll Deduction pre-tax or post-tax?: If the plan is pre-tax, the option to identify if the plan is reportable on the W-2 (as shown above) will appear. This option will only appear on health or supplemental health plans. If you are creating an FSA plan, options for this field will be Dependent Care Purposes or General Healthcare Purposes.
- If you have an existing (active or inactive) benefit plan set to pre-tax, and it needs to be post-tax, you need to end the plan and create a new one that will accurately reflect the change in deduction type. This is to protect against affecting historical payroll records adversely. To make a change to the payroll deduction, you will need to end the plan by entering today's date in the Plan Ends field, creating a new plan as post-tax, and then migrating the enrollments through the bulk enrollment tool.
- Reportable on the W-2?: Check the box if this plan is reportable on the W-2. This question will not appear when setting up supplemental plans with pre-tax deductions.
- When should this benefit deduction start in payroll?: Determine when the first payroll deduction should happen once an employee is enrolled in this plan. This setting will also define when the last deduction occurs after an employee is unenrolled from a plan, but the last deduction will be the one before the one indicated in the rule. Click here for more details.
- Does this benefit deduction happen every paycheck?: Check if this deduction happens every paycheck or not. If it skips some paychecks, you will need to determine below how often the deduction should be taken out. Please note the warning that if the deduction needs to skip some paychecks, you will need to manually suppress the deductions on the paychecks you want to skip when running payroll.
Once a deduction is approved in Payroll for a specific benefit plan, Payroll Deduction fields will no longer be editable for that plan. If you need to make edits to plan settings, you will need to end the current plan and create a new plan.
Do you have employees that need non-benefit deductions? Visit this guide to learn about how to set those up in BambooHR.
End or delete a benefit plan
If you have payroll history tied to a benefit plan, you will only be able to enter an end date in the plan's settings to preserve the data history.

If the plan does not have payroll history, simply hover your cursor over the plan and click on the trash icon that appears to the right. Deleting benefit plans will remove all ability to manage that deduction, and employees will automatically be unenrolled from the plan.
Extend a benefit plan
As you use BambooHR Payroll, we recommend extending a plan's duration (not end date) if you want to continue using a benefit plan that is already in use and will be ending. The following steps show two ways you can extend a plan.
One way is to create a new plan by duplicating the existing benefit plan for the new coverage period. You can do this by hovering your cursor over the plan and clicking on the duplicate icon. This will take you to a pop-up modal that asks you if you are recreating a plan for next year's open enrollment. If yes, choose the first option to have the plan recreated/duplicated. Note that the plan selection dropdown menu is automatically populated with the name of the plan you are duplicating. This is a helpful way to continue a benefit plan year to year, especially for open enrollment.
Clicking Continue to Duplicate Plan will copy over the plan details from the previous year, but you will be able to change the start date and end date, as well as make any additional necessary changes. However, there are some limitations to what settings you will be able to edit (see table below).
Once you save the new plan, you can use the bulk enrollment tool to enroll your employees in the new plan.
The other way is to update last year’s plan through the +Add New Plan button. Please note when you select +Add New Plan, you will see the same modal that pops up in the plan duplication process (as shown above). If you want to recreate an existing benefit plan and edit its settings for the new year, simply select the plan type* and then choose the existing benefit plan from the dropdown menu.
*You will need to have at least one existing benefit plan under the plan type you are recreating a benefit plan for. In the example above, the medical plan type has existing plans, from which I chose Select Health - Premium for the new year.
The following settings are not editable when copying over an existing plan by clicking Continue to Duplicate Plan or Continue to New Plan. If you need to edit those settings, we recommend choosing the second option in the pop-up modal to create an entirely new plan.
Plan Type | Settings |
---|---|
All plan types (Ben Admin only) |
|
Medical, dental, and supplemental health |
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Vision |
|
Retirement |
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FSA |
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Life Insurance |
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Disability |
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Other |
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BambooHR does not collect and remit payments for third-party vendors for any benefit plans.