Bamboo Payroll™ FAQ

Does Bamboo Payroll integrate with accounts payable software?

Bamboo Payroll does not currently integrate with any accounts payable software; however, your Payroll Specialist can generate a report to export this information for you. Exporting a GL ledger is simple to receive and import into other software programs. Reports can be requested as one-time or recurring.

How does reporting work?

Each time a payroll is run, a series of standard reports is generated in Bamboo Payroll (payroll register totals, check stubs, department totals, etc.). Your payroll specialist can generate any payroll-related report you need in the format that you need (excel, csv, etc.). This is one of the benefits of service-oriented payroll. Custom reports can be created as one-time or recurring.

What happens if I have questions?

Your dedicated Payroll Specialist is the best resource for all of your payroll related questions because they are APA-Trained payroll experts who learn your payroll as well as you do. They also work in your time zone, so they should be available when you need them. You can also send your questions to and we will create a support ticket for you. If you have general questions about BambooHR in general, our Support Heroes can assist you.

How do I track bonuses or commissions?

We can build standard tables to house this information (Job tab) that will sync with Bamboo Payroll. Please note, these standard fields cannot be edited nor can other custom fields/tables sync with Bamboo Payroll.

How do I set up Bamboo Payroll?

Once Bamboo Payroll is added to your account, you will go through a mandatory Payroll implementation. This is separate from your BambooHR implementation, though your HR implementation gets you most of the way there. For those switching mid-quarter, we assume responsibility for the remaining payments & filings for the current quarter which helps you break ties with your current payroll provider faster and eases the tax burden of changing payroll providers. We also conduct a mini-audit on the open quarter to ensure accuracy prior to reporting for that quarter. These audits save your company from the risk of tax penalties. Payroll implementation takes about 3 weeks on average, depending on the complexity of your payroll.

How does time tracking work within Bamboo Payroll?

We recognize that there are billions (ok, probably hundreds) of time tracking options out there, and infinitely more time tracking needs such as scheduling, government reporting, and multiple options for time recording. We want you to be able to use the best solution for your company, but make it easy to get the data to Bamboo Payroll. You can implement one of our great partners (sold separately), import data through our approved hours importer (super easy), or set up your own integration through our open API (approved hours endpoint).

For those of you who are interested in time and attendance, here is our list of recommended partners:



When do I have to submit payroll?

2 days prior to check date by 3:00 PM CST. Next day direct deposits are available for an additional fee per run; however, we want to keep next day deposits reserved for emergency scenarios rather than ongoing processing.

What does the tax service (included in Bamboo Payroll) include?

Preparing and filing of tax reports, payment to applicable agencies of quarterly and annual payroll taxes, filing of state specific new hire reports, access to all filed reports in your account, creating of W-2 forms for employees, and access to tax advisement by your APA-Trained payroll specialist.

Can you pay contractors?

Yes, contractors just need to be setup in BambooHR and setup to be “Included in Payroll”. Once included, all of their payroll-related information will sync with Bamboo Payroll and they will show up in the power grid. Please note that if you have contractors that are not run each month, then you will not be billed for the months they are not paid. For instance, if you have contractors who are paid quarterly, you will only be billed for the months that their quarterly payroll is included in the payroll run.

Is direct deposit available?

Yes, direct deposit is easy to set up. Employees will be able to add up to four bank accounts for direct deposit (or you can manage this yourself by changing Employee Access Levels). They can include percentages or dollar amounts. You can print physical checks (e-signatures available) on any printer and any check stock. We also set up unlimited payments directly to agencies as third-party payments such as garnishments and child support.

Do you integrate with 401(k)?

We have a 401(k) solution called PlatinumRetire. However, if you’d like to keep your existing provider, your payroll specialist can build the per payroll export file + census file for you to submit to your plan administrators.

How many pay rates can you handle?

We track one base rate for any employee type in BambooHR. 3 additional pay rates may be added on the Bamboo Payroll side; however, there is no limit to pay rates when importing hours worked data from your time tracking provider (these are reflected only on the power grid for each payroll run).

Does Bamboo Payroll handle state required New Hire reporting?

Yes, we will file New Hires electronically for those states that support it, others are filed on paper.

Will you provide a W-4 library for individual states?

There is an HR online resource located on the dashboard when logged into Bamboo Payroll that you will have access to.  Within this library, you will be able to obtain the most recent W4’s per state.

Do the employee's tax exemptions auto-fill from the e-signature W4 document they fill out in BambooHR upon onboarding?

Not yet. :) We will announce when this changes in the future. W4 and state withholding information will need to be entered separately into the Pay Info tab. Your payroll implementation process should capture the bulk of these at the start. Ongoing changes should be managed by employees on the Pay Info tab in BambooHR. The appropriate tax state(s) are selected for the employee by the admin/account owner when adding the employee via the new employee form. We suggest having an onboarding checklist item for the employee to fill out their exemptions once they login to BambooHR.

Do benefits deductions sync with payroll?

Yes! All employee deductions will sync with the appropriate per payroll amount. Specific pre-tax/post-tax designations can be configured once the deductions show in payroll. Deductions that follow a different frequency from the employee’s pay period (ex. 401(k) is deducted only once per month for an employee who is paid semi-monthly) can be set up as such in BambooHR when adding the plan to a benefit group.

Does PTO sync with BambooHR?

Yes! Approved PTO requests sync to the applicable payroll run(s) based on the dates requested. PTO requests only sync for hourly employees since PTO hours are not paid out to salaried employees.

Can I run off-cycle payrolls in Bamboo Payroll?

Yes, with the assistance of your payroll specialist who will make sure it is processed correctly. You will also have the option to process deductions on off-cycle payroll runs or to remove deductions.

Does Bamboo Payroll handle fringe benefit deductions?

Yes, we can accommodate fringe benefits.

Does Bamboo Payroll run reports for ACA Compliance, specifically Employer Shared Responsibility (ESR) tax reporting, is it included with your payroll service?

ACA compliance is an additional service, at an additional cost. Your payroll specialist will also work with you/advise you on accuracy and proper reporting.

Can we process manual checks (for termination, etc.) in Bamboo Payroll?

Yes, your payroll specialist can assist with the processing of manual checks.

Are there any other potential fees besides the ongoing fees?

Yes, we charge additional fees for the following services which are typically more rare and labor intensive (fees are subject to change at any time without notice):


  • Next Day Direct Deposit Processing: $40

  • Total Tax Filing <2 days processed: $40

  • Direct Deposit Reversal Request: $40

  • Direct Deposit Reversal Reject: $20

  • Direct Deposit Reject Fee: $20

  • Direct Deposit Correction Fee: $20

  • DD Reject/Correction Fee 2nd Notice and Thereafter: $35

  • DD Trace Request: $20

  • Stop Payment Fee: $40


  • Quarter End/Year End Corrections/Amendments: $200

  • W2 Corrections (per employee): $17.50

  • SSN Corrections: $35


  • Total Tax Filing NSF: $135

  • Direct Deposit NSF: $135

  • Billing NSF 1st Time: $60

  • Billing NSF 2nd Time: $90

  • Billing NSF 3rd Time and Thereafter: $145

Printing, Shipping, and Reporting:

  • W2 Print and Ship: $2 per form

  • Payroll Printing: 10% of PEPM, billed separately

  • Custom Reports: $150-$250

  • General Shipping: varies based on location