Payroll FAQ

What are the most common frequently asked questions for running payroll in BambooHR?

Table of Contents


Have more questions about what data syncs with Payroll? Check out this FAQ!

Payroll Transition

How do I log into TRAXPayroll if I'm no longer a customer and need to access my payroll reports?

We are sad to see you go, but we understand you still need access to your payroll data! To log in to TRAXPayroll and retrieve this information, visit our website and scroll down to the Support section at the bottom. Click on the TRAXPayroll Login link. 

What does this new product update mean for my current payroll process?

This new product update brings a range of exciting features and enhancements to streamline and simplify your payroll process. We have taken the features you know and love from TRAXPayroll and moved them to BambooHR while updating them to create a more intuitive user experience, improve accuracy, and increase automation. You can expect a more efficient and enjoyable experience overall. Here are some key items we’ve enhanced in BambooHR Payroll:

  • Edit Payroll: We’ve consolidated the two-step edit payroll process down into a single, easy-to-complete step. 
  • Extra Pay: You now have the option to add an unlimited number of extra pay items right to employees’ profiles or directly in Payroll.
    • Recurring Extra Pay: You can now customize how frequently extra pay occurs (monthly or every paycheck).
  • Seamless Hours and Deductions: Once you import hours, approve hours, or add benefits, you can feel confident they’re flowing directly into BambooHR Payroll without any additional work on your part.
  • Global Overrides: Set a custom tax rate for all employees by state (in addition to federal).
  • Off-Cycle Payrolls: Easily create manual payrolls and manually adjust salaried employees' regular hours.
  • Adjust Rates: Manually adjust overtime (OT) and double-time (DT) rates inside BambooHR Payroll.
  • Payroll Reminders: Set and review payroll reminders at every stage of the payroll process (pre-payroll, Edit page, Review page, post-approval).
What will I need to log in to TRAXPayroll for?

While a majority of your payroll run should be handled in BambooHR, there are still a few reasons why you may need to log in to TRAXPayroll: 

Eventually, these features will be a part of BambooHR Payroll. As of now, you will continue to have access to TRAXPayroll.

Will this affect how my taxes are filed?

No. There will be no interruption to your taxes, and BambooHR will continue to file taxes on your behalf.

What other questions have other payroll admins asked in regards to this transition?

You asked, and we have answered...hundreds of questions. Click here for all of the questions payroll administrators just like you have asked us about to ensure a seamless transition to BambooHR Payroll. 


General Administrative

Does TRAXPayroll work in all browsers?

Yes, you can find supported browsers here.

I completed the Getting Started Survey and expressed interest in a custom pay cycle data report. Does this count as my request?

No, you will receive an email that will explain a request form needs to be completed and it will provide a link to the request form. For ease, you can use this form link to submit your request.

I've completed payroll implementation. What are my next steps for managing my payroll account?

Congratulations on making it through the entire payroll implementation experience and running your first payroll with BambooHR Payroll! Now what? Download the resource below for more information on your next steps and how to maintain a clean and compliant account. 

Do you handle garnishments?

Yes, you can set up garnishments for free in BambooHR. If you want BambooHR to collect and pay garnishments on your company's behalf, we can also do that as an additional payroll service. Garnishments are a per payroll cost if you want BambooHR to collect and remit the funds. Some clients will set up a garnishment processing fee deduction to pass the cost back to the employee.

Do you print checks?

No, we do not print any checks. We are a green company and do not take on the liability of having your check stock in our offices. However, we offer the ability to print checks on-site directly from the system so that you do not have to wait for a packet to arrive and pay for shipping and postage. You can print checks in TRAXPayroll by going to the Reports tab and clicking on the Paper Check option in the Pay Stub box. From there, click on the applicable employee's name to see their printable check. Print the check on your company check stock. Click here to learn how to assign check numbers, and alter the check's configuration to match your company stock.

We work with a company, CTP Solutions, that can print checks for an additional cost. Please note we do not have an integration with their system, but they are available to print checks. Please contact them directly for more information. 

We recommend using pay cards to avoid paper checks for employees who do not have a direct deposit. While TRAXPayroll does not offer pay cards, you are welcome to contact any vendors that offer them. Companies like Rapid, Wise, or Chase are examples of companies that offer pay cards, though we do not partner with any of themPlease be considerate of your state laws with regards to requiring employees to be paperless.

What workers' compensation carriers do you work with?

We have Worker Compensation Premium Estimate reports that you can use to report your payroll to any carrier. We also offer the pay-as-you-go option with Amtrust, Hartford, or Travelers.

Do you integrate with Quickbooks or other accounting software programs?

We can build a general ledger report for Quickbooks in a .iif file or any other accounting software. You can download the custom report and upload it directly into Quickbooks to book your accounting. Quickbooks online requires a third-party upload tool to make it work. Please note all custom reporting has a charge of an additional fee.

What are some tips for preparing my account for payroll?

Check out this help guide for more data tips and tricks to set up your account and employee information before running payroll. 


Employee Information

Where can employees see paystub information in BambooHR?

The Pay Info tab will appear on the employee profile once they have an assigned pay schedule on the Job tab. Your employees will have access to view a quick summary of their most current paystub and their paystub history. 

Employees can also click on the nifty trend graph to view past paystub summaries and sort their pay history. It is intuitive, so you can probably let them figure it out themselves—time saved!

Any time a new paystub generates in TRAXPayroll, the pay information from that paystub will appear in BambooHR.

What if someone does not have a direct deposit account?

We recommend that clients print a check for those employees who do not have direct deposit.

Additionally, we recommend using pay cards to avoid paper checks for employees who do not have direct deposit. While BambooHR does not offer pay cards, you are welcome to contact any vendors that offer them. Companies like Rapid, Wise, or Chase are examples of companies that offer pay cards, though we do not partner with any of themPlease be considerate of your state laws with regards to requiring employees to be paperless.

What if an employee didn't receive their direct deposit on pay day?

There are several reasons an employee's check may be delayed or not deposited. The most common reason is when incorrect routing and account numbers are used. If this is the case, be sure to update the employee's bank account information in BambooHR as soon as possible. 

When a direct deposit is not received, BambooHR will be notified by the bank 2 business days following the pay date. At that time, we will reach out to your company contact to share details and payment options. In the meantime, we recommend having the applicable employee reach out to their bank's ACH department, who can tell them if they can re-route the funds to the correct account. 

We highly recommend waiting until we send you the direct deposit failure notice before you pay the employee any other way. For example, if you pay the employee through an off-cycle check and the bank reroutes the original deposit to the employee's correct account, you risk double paying the employee and will have to recoup the overpaid funds outside of payroll. However, the decision and risk of paying an employee before we reach out about a failure notice are ultimately up to you and your company.

How do my employees receive their year-end W-2?

All W-2s and 1099s are set to paper by default and will get mailed out to the employee's home address when ready. However, employees with access can elect for a paperless W-2 by toggling on the Go paperless and get my tax documents exclusively online option at the bottom of their taxes section, under the Pay Info tab. BambooHR will send out an email to all employees when their W-2s are available online. Admins have access to all W-2s through the Reports tab in BambooHR.

All terminated employees (and the employees of terminated clients we are processing year-end for) will receive a paper copy regardless of their election.

For more information about year-end tax documents, visit the Tax Document FAQ.

What are the fees associated with W-2's?

To learn more about the fees associated with the W-2 form, please refer to the additional payroll fees.


Running Payroll

How do I correct an incorrect payment made to an employee?

When a payment is incorrect, it's important to get it corrected as quickly as possible. Please note there are fees associated with voids and reversals. Use the appropriate pay types and deductions to ensure year-to-date totals are also corrected. Employees should be informed so they're aware of the correction method.

If an employee was overpaid, consider the following options after notifying the employee:

  1. Collect the overpayment on the next paycheck, using the appropriate deduction or negative pay type. 
  2. Recall the funds through the employee or via a reversal. Once the payment is recovered, process a void through Payroll Support and run an off-cycle payroll to record the correct payment.

If an employee was underpaid, consider the following options after notifying the employee:

  1. Add the underpayment to the employee's next paycheck, using the appropriate pay type or negative deduction.
  2. Process an off-cycle payroll for the underpayment. Consider suppressing deductions to avoid over-withholding.
  3. Process a void through Payroll Support and run an off-cycle payroll to record the correct payment. If you've collected the incorrect payment, pay them the new net amount. Otherwise, make sure to override the off-cycle payroll for a printable check so they aren't getting paid a portion again. Instead, write the check for only the net difference between the incorrect and corrected check.
Does the system adjust (prorate) for salary employees who are terminated or start within the pay period?

BambooHR Payroll will flag if an employee is hired or terminated within the payroll. If a salaried employee is hired mid-pay period, you will be prompted to prorate the employee's salary. Click here to learn more. 

If an employee gets a pay increase during the pay period, will the system re-calculate the salary based on the number of days at the old and new rates?

No, the system only calculates the per pay period salary for each pay cycle. You can manually calculate the difference and updated wages on the Edit page.

How do I correct incorrect deductions withheld or incorrect deduction year-to-date totals?

Most incorrect deductions can be corrected in an off-cycle payroll or on the employee's next paycheck. To make corrections, follow these steps in your selected payroll:

  1. Click on the employee's name within the Edit page of payroll to access their Payment Details page. 
  2. Scroll down to the Deductions section and click the pencil icon next to the deduction you need to correct. Then enter the correction amount within the Employee pays field. Don't forget to include current pay period deduction amounts in your calculations (see example below). Entering a positive deduction amount will reduce the employee's pay, so you can only make this correction during a payroll where the employee also has earnings greater than their deduction amounts. Entering a negative number will reimburse the employee and likewise correct their year-to-date total for that deduction.
  3. Click Save Changes > Calculate and continue to the Review page. View the employee's unapproved paystub within the Paystubs section on the Review page to verify deductions and year-to-date totals are correct before approving.

For example: If I originally withheld $25 for a deduction that should've been $20, I'd enter negative $5 (-5) as the Employee Pays amount to refund the difference to the employee on the off-cycle payroll. However, if I do this on a regular payroll run, I'd likely enter a positive $15 (15) to account for the $20 deduction for this payroll plus the $5 refund.

Does payroll in BambooHR account for Virginia's overtime requirements?

Currently, BambooHR does not automatically calculate this since they are applied according to your own company guidelines and tax laws. You will need to calculate these totals for your employees and add them as extra pay when running payroll. Please be sure to refer to Virginia's state tax website for overtime wage rules. 

Since the calculations are required by a 40-hour workweek, you could opt for biweekly or weekly pay frequencies for hourly employees (workweek may be determined by a company, i.e., Monday - Sunday or Sunday - Saturday, etc.) as this will make the calculations a bit easier. 

Once you have determined the dollar amount, you will need to add this as an extra pay type in Payroll by selecting the Additional Overtime Pay wage type.. 


Taxes

Have specific questions about Tax Documentation? Click here for more information!

Will supplemental wages (bonuses) automatically be taxed at the correct federal rate?

You will need to manually adjust supplemental wage types such as bonuses manually for all employees through a global override or individually on the employee's Payment Details Page during the run payroll process.

How do I handle an individual extra pay amount that needs a tax adjustment without running an entirely new off-cycle payroll?

If you need to adjust a tax rate for an individual pay type or set of pay types outside an employee's regular payroll, you can do so by adding a paycheck to the employee's payroll record on the Edit page and then adjusting the taxes within the Payment Details Page of that section. 

How can I calculate gross-up taxes to ensure my employee receives the full amount of net pay promised, even after taxes are withheld?

We recommend using Business.org's Gross Up Calculator to help you calculate and find these estimates. Business.org uses Symmetry, the same trusted tax engine BambooHR® Payroll uses to ensure the most accurate payroll for your company. For more information on how to use this calculator, click here!

Will the changes I make to my employee's taxes on the current payroll affect future payroll runs?

No. Changes made on the Edit page during the run payroll process are one-time updates that will only affect that payroll. If you wish to permanently change an employee's withholding, visit their Pay Info tab and update it on their record. If you wish to make a more permanent change to your company tax account, visit Company Tax within Settings > Payroll. 

How are the fields within the post 2020 W-4 reflected in BambooHR?

Click here for a breakdown of how the post 2020 W-4 translates to employee fields in BambooHR Payroll. 

I have received an updated tax notice from a state my company is registered in. What do I need to do?

If you receive a tax notice from the IRS or a state agency where you are registered, please email Payroll Support and attach the tax notice to the email. Our Payroll Services team will make the necessary updates to your account. 

Does the system allow you to designate one state or another (or both) to withhold state payroll taxes?

You can designate which state taxes are paid out of. An employee can only have one state per pay period assigned.

Why was my employee taxed at such a high rate on their paycheck compared to previous paychecks?

Taxes are calculated on the taxable income of the current pay period, not the annual amount. As a result, higher paychecks may be taxed at a higher rate if the higher amount puts the employee in a higher tax bracket.

Why are my employee's taxes higher starting in the new year?

Generally speaking, certain taxes have wage bases that start over each calendar year, which is why taxes are higher at the start of a new year. FUTA tax is higher and this is as expected because FUTA restarts each calendar year. FUTA tax applies to the first $7,000 you paid to each employee as wages during the year. Here is this IRS resource providing more information on this topic. 

Social Security has a changing wage base each calendar year.  Here is this IRS resource providing more information on this topic.

Can I tax an employee in more than one state? 

You can only tax an employee in one state during the pay period. If an employee moves mid-pay period, you can change the job location on their Job tab, the state in which taxes are withheld on their Pay Info tab, and run an off-cycle payroll to capture the second state. 

Does BambooHR Payroll handle Social Security wage base limits and Medicare excess wage rate changes? 

Yes! BambooHR Payroll will automatically halt employees' Social Security contributions once they hit the wage base limit for the year. We will also increase their Medicare rate to 0.9% once the excess wage limit is met, according to the IRS. When the new year begins, we'll automatically start withholding Social Security taxes again and revert Medicare to 1.45%.


Deductions

Does payroll in BambooHR push out the 401k deferrals to 401k vendors?

BambooHR can send a custom file feed to any 401k vendor as long as they accept electronic file feeds. Please note all custom reporting includes an additional fee. If you are interested in a custom 401k file feed, complete this request form.

Does Payroll work with pre-tax administrators (FSA, transit, commuter, dependent care)?

No, but you can set up uncollected deductions for all of these and then pull contribution reports for them after you approve payroll.

Can Payroll in BambooHR handle Roth and catch-up 401K deferrals in addition to the regular deferrals?

Yes, the system will automatically account for an employee’s catch-up contribution amount if the employee is at or above the age of the catch-up limit. The max contribution will also automatically be applied for the current year based on the global limit amounts set by the IRS. The 2024 max contribution limit for employees 49 years old and under is $23,000.00; for over 50 years old, it is $30,500.00.

Read more about automatic 401k maximums in payroll under "Does payroll automatically cap 401k and HSA deductions at their annual maximums?" in this guide.

Does payroll automatically cap 401k and HSA deductions at their annual maximums?

BambooHR does automatically calculate and cap 401(k) contributions at the annual maximums based on the IRS limits for an employee's age, and cap HSA contributions at the annual maximums based on the IRS limits for the employee's coverage level.

How are Roth 401k plans calculated if it's showing a percent of the employee's gross pay when it should be post-tax?

Roth contributions are calculated based on gross pay but deducted from net pay, which is why the plan setup shows a percentage of gross pay. "Gross" refers to the amount used to calculate the deduction and/or employer contribution amount. The Roth plan type will indicate it is post-tax and report to the W-2 accordingly.


Payroll Reporting

Where can I go to find Approved payroll reports?

There are three places you can go to view approved payroll reports: 

  1. Approved Payroll Summary page in BambooHR.
  2. Payroll Reports in BambooHR > Reports.
  3. TRAXPayroll Reports tab under Pay Cycle and Date Range.

For more information on how to navigate payroll reporting, click here!

Where can I find unapproved payroll reports for reconciliation during the payroll process?

While running payroll, you can download unapproved payroll reports on the Review page by clicking Preview Payroll Reports. You also have access to download the data within the Payroll Details section of the Review page. 

For more information on how to navigate payroll reporting, click here!

Why are some payroll reports under Standard Reports and others under Payroll Reports in BambooHR?

This is a great question! The payroll reports found under Reports > Standard Reports pull data from your employee's profile information specific to payroll. These reports are great for pre-payroll activities and making sure you are in the clear with employee data before running payroll. These reports are also compatible with standard reporting functions like sharing, Favorites, Folders, and more. 

The reports found within Reports > Payroll Reports are specific to running and approving your payroll. These reports only become available after a Payroll Admin has approved payroll, and they are not subject to normal standard reporting functionality, as mentioned above. All reports in this section can also be found in TRAXPayroll. For more information, click here.

Will custom access payroll users with View Payroll Reports enabled automatically have access to the payroll reports in Reports > Standard Reports?

The View Payroll Reports setting will only allow access to the reports found on Reports > Payroll Reports in BambooHR only.

Full Admins will still need to share payroll reports found within the Standard Reports section of BambooHR to custom payroll access level users. Payroll Admins will be able to automatically view standard payroll reports, but will not be able to share them with custom access level users.