Run Payroll in BambooHR

This article provides a comprehensive guide on running payroll in BambooHR, covering the entire process from starting payroll to approval. It outlines key steps, including starting payroll, editing employee records, reviewing payroll, and approving payroll. Users are informed that any changes made to employee data before starting payroll will be reflected in the current run, while subsequent changes will require resetting payroll. The article emphasizes the importance of verifying employee information and resolving any errors prior to payroll approval. Additionally, it offers resources for further assistance and highlights the benefits of BambooHR Services in streamlining payroll processes. Overall, the guide aims to facilitate efficient payroll management for users.

  • Jul 9, 2026
  • Knowledge

Title
Run Payroll in BambooHR
Article Text
Run payroll is part of Payroll that is an add-on feature.

If you do not have BambooHR Payroll and are interested in a demo, click here and fill out the form!

How do I run payroll in BambooHR?

Purpose: The purpose of this guide is to outline the entire run payroll process and features from starting payroll to approving it in BambooHR. All updates made in BambooHR will be saved in TRAXPayroll and vice versa.

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Table of Contents

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Need to upload extra pay before starting payroll? Click here for more information!

Start Payroll

Please note that starting the payroll process will take a snapshot of the employee data as of the current date. Therefore, you will want to make any essential changes or additions to your employees before running payroll. If you have an employee data change that is effective after starting payroll, it will not automatically be included in the current payroll run. Instead, those changes will be effective in the payroll following the effective date, or you can reset your payroll or the employee record on the Edit page to include those changes as long as the start dates align with the start date of the pay period.

To begin the payroll process, navigate to the Payroll tab, locate the pay cycle you want to run, and click Start Payroll to validate your company and employee information.

If the system detects an employee-level error, a modal will pop up, and you will have the option to handle the error(s) by clicking Fix Errors or disabling payroll for the employee by clicking on the X. The Fix Errors button will take you to the People Being Paid page, where you can update employee information.

Once you fix the error(s), go back to the Payroll tab and click Start Payroll to get started with running your payroll. If you pass the data validation and sync step, you will get to the next page, and this step is where you can edit your payroll.

If you go back to the Payroll Center once you start your payroll, the button will turn into the Continue Payroll button for you to click on and pick up where you left off. You will also notice a Reset Payroll button appear underneath. This lets you reset your payroll data and start fresh without opening the payroll run. Clicking Reset Payroll will also remove any edits made to the current payroll, so keep that in mind!

For more detailed information on starting payroll, click here!

Edit Payroll

The Edit page allows admins with payroll permissions to edit payroll all in one place. You can view important pay cycle information in the header of the page, and use the table below to make changes to individual employee records for the current pay cycle before calculating payroll. Check it out:

  1. Pay Date: Employees will receive their paychecks on this date.
  2. Due By: Payroll must get approved by this date and time in your time zone. Payroll is due no later than noon PST on the due date.
  3. Pay Schedule: This field displays the name of the pay schedule you are currently running.
  4. Pay Period: The start and end dates of the pay period will appear here.
  5. Gear Icon: Click on the gear icon for the option to reset your payroll or apply global payroll overrides. Keep in mind that resetting payroll clears all edits made to the payroll.
  6. Prorated Wages: If you add or terminate an employee mid-pay period, you'll see a banner to adjust their hours. A banner will also appear if an employee has a mid-period pay change or takes unpaid time off, prompting you to review wage adjustments.
  7. Filter: You can use the Search field to filter information by an employee's name or department. If you apply a filter, you can sort the filtered data by Employee or Gross Wages. For additional filters, click the filter icon next to the Search bar. A modal will display for you to sort the payroll table by our standard filters, Tax Type, Pay Type, and Overtime Status. Global Overrides will still apply to all employees even if the payroll table is filtered.
  8. Employee Count: This is the number of employees included in the current pay cycle. The count will update in real-time when you search for an employee or filter.
  9. Payroll Reminders: Click on this link to view outstanding or completed payroll reminders. The payroll admin can also add, edit, or mark payroll reminders through this modal.
  10. Exclude Employees: Clicking on this link will display a modal of excluded employees for the current payroll run. If a list of excluded employees populates, you can fix their errors and add them back. Please note this will not appear if all employees are included.
  11. Employee: The Employee column lists each employee (alphabetically by Last Name, First Name) in the pay cycle along with their department and annual salary based on their active wage record. You can click on the Employee header to sort by First Name, Last Name, or vice versa. You can also click on the employee's name to open the Payment Details page, where you can make additional edits to their paycheck for the current payroll run.
  12. Hours: You can manage your employee's working hours and rates within the Hours column. Click to sort the payroll by the amount of hours in ascending or descending order. This column displays the following hour types:
    1. REG: Regular hours (includes time & attendance data and multiple pay rates for hourly employees and imported hours)
      1. The total regular hours are determined by the Hours Per Week setting on the employee's active compensation record. The total will automatically adjust if the employee has approved time off or holiday hours. Keep in mind, if you manually adjust regular hours for a salaried employee, the total calculations of regular hours will not automatically adjust for time off or holiday hours.
      2. For salary employees, the system automates wage calculations for mid-pay period pay changes, provided the employee's Pay Type is Salary at the start of the Pay Period, their hours per week are set to 40, their Salary Pay Rate changes during the pay period with consecutive dates and no gaps, and the change was an Update or New Entry (not a Correction). This automation applies to employees working a 40-hour work week.
    2. Any approved time off hours (by category)
      1. These hours are a breakdown of regular (REG) hours.
    3. Holiday hours
      1. These hours are a breakdown of regular (REG) hours. For more information about holiday hours, please review this help guide.
      2. If you've awarded employees time off on a holiday, those hours will automatically populate under the Holiday hour type.
      3. If your employees earn a multiplied rate for working on a holiday, those hours will automatically populate under the Worked Holiday (rate multiplier) hour type. Please note, the Worked Holiday hour type is only available for hourly employees. These rates will automatically populate if the employees are tracking time with BambooHR Time & Attendance, if you've imported hours worked, or if you've manually added the hours on the Edit page.
    4. OT: Overtime hours
    5. DT: Double time hours (nonexempt employees)
  13. Gross Wages: The Gross Wages column displays the employee's gross wages for the pay cycle based on their active compensation record. Clicking on the Gross Wages column will remove the sort by Employee name and sort the records in ascending order from smallest to largest. Clicking on the column again will reverse the order from largest to smallest.* While gross wages will be automatically calculated for hourly employees, you can edit gross wages for your salary employees.
  14. Extra Pay: The Extra Pay column allows you to add, edit, or remove standard and custom extra pay for each employee during the current payroll run. Click to sort the payroll by the amount of extra pay in ascending or descending order. The best part? You can add unlimited pay types to an employee's record.
  15. Edit Page Totals: To make the payroll process more efficient and accurate, the payroll totals will display at the top of the Edit page. Click the arrow dropdown next to Totals to display total hours (by type), total wages, and total extra pay (by type). If a filter is applied, you will only see the total for the filtered group of employees.
  16. Paystub Notes: Once you've added at least one paystub note, you can review and edit those notes by hovering over the note icon found on the employee's photo.
  17. Event Banners: If an employee is hired, terminated, has a pay change, or uses an unpaid time off category during the pay period, a banner will appear to notify you.
  18. Three-Dot Menu: Click the three dots on the employee record to add a paycheck, reset the employee's payroll data, or remove the employee from the current payroll run.
  19. Calculate Payroll: Once you have made all edits to payroll, click Calculate Payroll to view the Review Page, where you can check your payroll before approving. Please note that clicking Calculate Payroll does not approve payroll. If you run into errors and need help, click here.
  20. Changes Saved: Any changes made to payroll will be automatically saved, as indicated next to the Calculate Payroll button. No need to worry about saving your edits manually or losing your progress!
  21. Pay Cycle ID: Your Payroll and Pay Cycle ID will display in the bottom corner of the Edit page. The first four digits are your company payroll ID, and the last seven are specific to the pay cycle. You will need both ID numbers if you call into Support.

*If you sort the Edit page by gross wages and an employee has multiple paychecks, BambooHR will calculate the combined total of paychecks for that employee before sorting to ensure the employee's paychecks are grouped together.

Need help managing your hours, pay rates, and gross wages during payroll? Check out this resource for more information.

Add paychecks

Do you need to pay out employee bonuses or create an additional check to tax wages separately from the rest of the employee's paycheck? You can add multiple paychecks within a single payroll run to an employee's record from the Edit page.

To add a check, hover over the employee's record, click the three dots on the right side, and then select Add Paycheck. A new Payment Details page will display, allowing you to add hours and wages, manage deductions, make the check printable, and leave a paystub note, if necessary.

Once the edits are saved on the Payment Details page, a new record line will show the additional check on the Edit page for the employee. The checks will be numbered in order. Each additional paycheck will also be displayed individually on the Approve page upon approval.

If you need to delete a check, hover over the check record and click the trash icon on the far right side.

Double-check you are deleting the right check number! Deleting Check 1 will remove the employee from the payroll run and delete any additional paychecks.

Reset, remove, & add employees to payroll

It is common for payroll admins to make adjustments to an employee record in the middle of running payroll. For example, an employee received a raise and you need to adjust their compensation table to reflect their new annual rate in payroll. Instead of having to reset the entire payroll for those updates to appear on the employee record, you can hover over the employee record, click on the three dots to the right, and then click Reset This Employee's Payroll to update their record with the new information.

You will be prompted to confirm that you want to reset the employee's payroll record. Upon confirmation, BambooHR will revalidate the employee's data. If there are any payroll errors found within the employee record, a new modal will appear, allowing you to fix any missing or invalid information. You must fix the payroll errors before you can reset the employee's record.

You can also remove employees from the current payroll run by hovering over the employee record, clicking on the three dots, and selecting Remove Employee. Again, a modal will appear, asking you to confirm the removal of the employee. The employee record will no longer appear on the Edit page, and the employee will be added to the Exclude Employee list. This list is where you can add them back into payroll if needed.

Employees who are removed from the current payroll run and employees who have payroll disabled on the People Being Paid page will appear in the Exclude Employee list. Please keep in mind the difference. Removing an employee on the Edit page is a one-time adjustment. Disabling an employee from payroll through the People Being Paid page will remove the employee from all future payrolls.

To add back an employee into payroll, navigate to the Exclude Employee list on the Edit page and click on the plus button next to their name. Payroll errors will appear next to the employee name if any new payroll errors are found. You must fix these errors before adding them back into payroll.

If you add an employee who previously had payroll disabled on the People Being Paid page, they will be included in all future payrolls moving forward.

Reset your payroll

Resetting your payroll will clear any edits made to the current payroll run, revalidate the payroll data, and populate any approved hours in BambooHR.

To reset your payroll, navigate to the gear icon on the Edit page, click the dropdown, and select Reset Payroll. If no payroll errors are found, you will return to the Edit page with a clean slate. If you were to navigate back to the Payroll tab, the Continue Payroll button would still appear; however, please note that payroll has been reset.

If any company or employee payroll errors arise, you must resolve the errors before returning to the Edit page. The process for updating errors is the same as fixing errors detected when starting payroll. If updating errors on the People Being Paid page, you will see a "Start Payroll" button, or you can return to the Payroll tab. In this instance, the "Continue Payroll" button will now show as a "Start Payroll" button since you reset the payroll data and updated data outside the payroll run, impacting your company or employee's account information.

Review Payroll

Upon calculating payroll, you will land on the Review page, where you can reconcile the edits made to the pay cycle. Reconciliation consists of the following:

  • Checking amounts needed to fund the payroll
  • Checking amounts your company will be responsible for dispersing
  • Identifying and resolving discrepancies
  • Approving payroll with confidence

This page will include three main sections for you to ensure your employees get paid correctly and on time:

1. Summary chart: The Summary chart provides a high-level summary of funds required for BambooHR to process your company's payroll. The following amount breakdowns will appear:

  • View Breakdown: This is the total of taxable and non-taxable wages (salary, hourly, and extra pay) collected by BambooHR Payroll. The employee tax types used to calculate this total include 1099, W-2, S Corp - 2% Shareholder, H-1B Visa, and Expatriate. ClickView Breakdown to open the Gross Wages Breakdown modal. If applicable to your account, this modal will separate employee wages and extra pay into two tables, including a 1099 Wages table for all contractors and an Employee Wages table for all other employee tax types.
  • Total to be Electronically Transmitted: The amount of the payroll debit, including direct deposits, employee and employer taxes, collectible deductions, collectible garnishments (if any), and fees. Uncollected deductions, such as health insurance and dental insurance, are not included in the total debit. They stay in your bank account for you to distribute as needed. Checks to Print will also not show up under the total debit but will show under the Total Cash Requirement needed to process this payroll.
    • If a wire is required, this will be replaced with the total amount needed for the wire and instructions on how to set that up.
  • Checks to Print: The total payroll amount that will be paid out through checks. Clicking on View Employees will display a modal with all employees who will receive checks, their individual amounts, and the total amount to be paid through printed checks.
  • Cash Requirement: This is the total amount of all money needed in your company bank account prior to processing payroll. This includes the electronically transferred amount plus the amount being paid through printed checks.
  • Total People Being Paid: This number is the total count of people included in the payroll run. This section will also display the total amount of people excluded from the current payroll as a hyperlink. Clicking on that total will display a modal with the excluded employees. Keep in mind you will not be able to make changes to include an employee on the Review page.

2. Payroll Summary: The Payroll Summary section breaks down each part of payroll and displays the amounts by Funds We Collect vs. Funds You Are Responsible For. You can also view payroll reminders and payroll reports.

3. Payroll Details: The Payroll Details section includes the Paystubs, Taxes, Deductions, Extra Pay, Hours, and Payroll Costs tabs to help you reconcile payroll data at the employee level right from the Review page. You can easily filter the tabs to show specific employees and export the data as an Excel or CSV download. Click here for more information about Payroll Details on the Review page.

Once you have reviewed your payroll within the Review page, there are three buttons for you to select at the bottom of the page:

  1. Approve [Date] Payroll: Clicking on this button will initiate the Approve Payroll process. A modal will display for you to confirm that you are ready to approve payroll.
  2. Edit this Payroll: Selecting this button will take you back to the Edit page.
  3. Payroll Pay Cycle ID: The first four digits of the ID number are your company-specific payroll ID, and the last seven digits are the unique identifier for that specific pay cycle. You will need both if you need to call Support.

Are you running into errors at any point in your payroll journey? Click here for more information on how to manage them.

Approve payroll

Did you know you can run and approve payroll prior to your due date? This is a great option if you're going to be out of the office or if you have a busy week coming up. Just be sure that you take any date-specific data into account beforehand!

After clicking Approve [Date] Payroll on the Review page, a message will appear requiring you to approve the transfer of your funds. Clicking Approve Transfer for [Amount] will initiate a data sync to ensure all payroll information gets calculated correctly.

If there are no issues, you can click All Done to return to the Payroll tab in BambooHR or click Go to Payroll Reports to review your approved payroll reports.

You also have the option to view additional payroll reports in TRAXPayroll after approving payroll.

Curious about your payroll funding method and when your employees will get paid? Click here for more information.

If you select All Done, you will return to the Payroll tab, and the payroll information box will have a stamp of "Approved," indicating that you have processed your payroll successfully. This view will disappear after the pay date, but don't fret! You can still access your pay cycle data through the Payroll History page after the pay date.

If it is before the 10:00 AM PT deadline, you will also see the option reopen your payroll. To access the Approved Payroll Summary page and view your employee's approved paystubs, click View Approved Reports.

If you need to make changes to a payroll that has already been approved. There is a very small window in which to complete this. Approved payrolls can only be reopened until the deadline of 10:00 AM Pacific Time on the due date. If you reopen payroll before the 10:00 AM PT deadline, you will have until 12:00 PM PT to make the final approval. Once that Reopen Payroll button has been removed a payroll can no longer be reopened. You can contact our payroll support team to discuss other possible options.

The Approved Payroll Summary page looks similar to the Review page when running payroll. However, this page now includes an "Approved" stamp.In the Payroll Details section at the bottom, you can view your employee's approved paystubs under the Paystubs tab. You can also click Go To Payroll Reports to navigate to the Payroll Reports page within the Reports tab to view approved reports.

Are you tired of manual, error-prone payroll that leads to late paychecks and frustrated employees? Does the thought of staying compliant with ever-changing tax regulations keep you up at night? You're not alone. Many businesses grapple with inefficient payroll processes that drain time, resources, and morale.

Our Solution: Our BambooHR Services team can help you create a streamlined, compliant payroll process that saves time and reduces risk. They also offer expert guidance on off-cycle pay, terminations, and compliance requirements.

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