Setting Up Payroll - Common FAQs

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Account & Security Settings

Do I need to complete 2FA (Two-Factor Authentication)?

Currently, only Homebase Payroll Admins require 2FA on their account, for security purposes. All other permissions levels and accounts are optional. 

To view instructions on how to setup two factor authentication, please review this article:  2 Factor Authentication Setup

How do I make my accountant/manager an admin?

1. Ensure they have a Homebase user account.
2. If not, add them to the Team Roster.
3. Adjust their permissions using this guide.

Why can’t I edit my employee’s information?

• Check Team Permissions under Settings > Team Permissions.
• If the employee’s invitation is pending, they must accept it before changes can be made.

How can I delete duplicate employee profiles?

If an employee has multiple profiles across different companies, this requires assistance from Homebase Support to properly merge or delete them.

Can I use the same email address for one employee across multiple accounts?

Yes you can however, the employee will receive an invite on their existing Homebase account that they must accept before you can make edits to their profile. Using the same email for multiple Homebase accounts will not merge the accounts or their data. Each account remains separate with its own permissions, payroll records, and settings. 

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Payroll Implementation & Setup

What does payroll implementation look like?

• A dedicated project lead will guide you.
• Homebase collects and loads employee & historical payroll data.
• Available training: recorded videos, webinars, and 1:1 walkthroughs.
• Setup can take as little as 5 business days (7 business days from your first check date).

How long does payroll implementation take?

It depends on company complexity: 3 business days to 2 weeks is our general timeframe.

Why do I need to sign certain tax forms (e.g., Power of Attorney)?

These forms allow Homebase to file and pay taxes on your behalf.

If I missed providing a payroll during implementation, how can I add it later?

You will need to contact payroll support who can assist with adding any missing payroll history.  

How do I set up remote employees?

To set up a remote employee:

1. Go to the employee’s profile in Homebase.
2. Click on the Personal Information tab.
3. Select “Employee Works Remotely” to designate them as a remote worker.
4. For more details, visit: How to Add an Employee to Payroll.

Can I send my payroll history after I run my first payroll?

No, payroll history must be added before your first payroll run in order to ensure that any limits are accounted for.  For example, if an employee reaches the taxable wage threshold for state unemployment, it wouldn't calculate anymore on payrolls.  That can only be determined by loading your payroll history. 

Why do I need to pay a ‘historical liability debit’ amount?

Homebase collects this amount to ensure that any unpaid taxes from your previous payroll provider are remitted on time.  For example, state unemployment tax deposits are due quarterly so your previous provider has likely not paid it yet.  We will collect this tax and your previous payroll provider should refund this for you.  If you know that your previous payroll provider already deposited those taxes, we can adjust the historical liability debit amount to reflect this.  Reach out to your payroll implementation project lead if you need this to occur. 

What is the ‘historical liability debit’ (HLD)?

The HLD represents tax liabilities accrued but not yet paid by your previous payroll provider.

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Payroll Costs & Billing

Will I be charged for inactive or former team members?

You can keep former or seasonal team members on your roster without incurring an additional fee simply for having them listed. Setting a team member to Inactive stops alerts and scheduling for that person while preserving their history.

• There is no extra charge just for making a team member inactive.
• Payroll fees per employee only apply to employees included within an active payroll run within a given monthly billing period.

When will I be billed?

The first business day of the following month.

Which account will my payroll fees be withdrawn from?

Review Settings > Payroll Settings to see the last 4 digits of your linked bank account.

Can I pay my payroll fees with a credit card instead of my bank account?

Yes, but actual payroll runs (Direct Deposits and taxes) must be paid from a bank account.

Can I pay payroll fees from multiple bank accounts?

Yes, Homebase allows for multiple bank accounts to pay your employees and payroll fees. The default bank account set will be used for regular payroll runs and Autopayroll.

You can add multiple bank accounts in Payroll Settings.

How do I change my payroll funding bank account?

Update it in Settings > Payroll Settings.

How do I change my pay date?

• During implementation: Speak with your project lead to request a change.
• After implementation: Call Homebase Support to modify your pay date.

How do I change my pay frequency (e.g., weekly, bi-weekly)?

Once the first payroll has been processed, pay frequency cannot be changed in the settings and you will need to contact Homebase via chat. 

Can my accountant pay my taxes instead of Homebase?

No. Homebase calculates and withholds tax amounts at the time of processing payroll.

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Employee Payroll & Taxes

How do I setup / how do I know which states have reciprocity?  

See Reciprocity Partner Guide.

How do weighted (blended) wage rates work in Homebase?

Note: See the Blended Wage Rates section.

I received a notice to calculate taxes for a specific state. What should I check?

If you receive notices to calculate taxes for a specific state, verify both the employee’s home address and the work location. Tax rules often depend on where work is performed and, in some cases, the employee’s resident state.

What to check

• Employee home address: Make sure it’s correct in the profile. An incorrect home state can trigger the wrong withholding or notices.
• Work location: Set the physical worksite address where the employee performs services. For remote staff, mark them as remote and set the correct work state.
• Registrations: You may need to register for state withholding and unemployment in each state where you have nexus or where employees work.

How to update

1. Go to Company > Payroll Taxes and add the required state(s) for employer accounts (withholding, SUI). Enter your account IDs once approved by the state.
2. Open Employees > Taxes and confirm both Resident State and Work State are correct. Complete any state-specific forms.
3. If there is a local tax (city/county/school district), add it where applicable.

After updating

• Reopen or refresh the payroll run so the correct state taxes calculate.
• For past periods filed incorrectly, consult your tax advisor about amendments.
• If you were using Homebase Payroll during the incorrect reporting then email taxops@joinhomebase.com to resolve.
• If you were with another payroll provider before Homebase you will want to contact them to correct/ammend reportings.

Notes

• Some states have reciprocal agreements; employees may owe resident-state tax while being exempt from work-state withholding. Configure elections accordingly.
• We can’t provide legal or tax advice; please consult a tax professional for your situation. For more info on State Tax Reciprocity, see here.

How do tip credits work?

Find more details in this article.

What taxes does Homebase file and deposit for me?

Homebase files and deposits federal, state, and local payroll tax. Copies of filed forms are available in your account.  You can also refer to this article:  Federal and State Payroll Tax Forms Filed By Homebase

Do you handle New York Paid Family Leave (NY PFML) & State Disability Insurance (SDI)?

Homebase deducts these amounts from employees but does not remit payments to carriers. The deductions will remain in your company bank account.  You must manually send payments to your insurance provider.  Please refer to this article:  NY SDI and PFL

Do you remit benefit and deduction payments?

No, all deducted funds remain in your company account. You must pay benefits manually, except for state-mandated child support garnishments which Homebase remits.  Please refer to this article on how to setup deductions:  Add/Remove a deduction

Does Homebase handle workers' compensation payments?

• If using Next Insurance, see this article.
• If using another provider, you must remit payments manually.

Does Homebase handle funding for my 401(k) contributions?

You can setup a 401(K) deduction on employees but Homebase will not remit the deductions to a 401(K) provider and Homebase will not report any deduction amounts to a 401(K) provider

Is there a 401(K) provider your recommend?  

Yes, we recommend using Guideline as that we may build a 3rd party vendor feed to this provider in the future 

Why isn’t federal or state tax withheld from my employee’s paycheck?

Check the following factors:

• Employee classification (W-2 vs. 1099 contractor)
• Exemption from federal or state withholding
• W-4 / State tax elections

How much tax do I have to pay per employee?

Taxes include:

• Employee-paid taxes (deducted from paychecks)
• Employer-paid taxes (company responsibility)

Is it required that I pay state unemployment taxes?

Yes, most employers must pay state unemployment taxes (SUTA) unless exempt.  You may want to check with an accountant or tax professional if you believe your business may be exempt from state unemployment.  The most common case for this are non-profite organizations.  

What are taxable wage base limits, and what taxes do they pertain to?

Taxable wage base limits cap the amount of an employee’s wages subject to payroll taxes.

How do I complete a W-4 and state tax withholding form?

Editing W-4 Information: Edit Personal Tax Settings.

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Payroll Processing & Payment

Can I send live check amounts via Zelle or CashApp?

Yes but you must make sure to run the payroll in Homebase to get the net amounts and to make sure the wages are added to the employees for tax filing purposes.  This can be done by selecting 'live checks' while running payroll and then paying the net amount using applications Zelle or CashApp.

How do I print paper checks?

Note: See Printing Paper Paychecks.

Where do I purchase check stock for printing payroll checks?

Multiple vendors sell check stock compatible with Homebase’s “check on top” style PDF. Learn more here.

What time do direct deposits (DDs) hit employee bank accounts?

Usually the morning of payday, depending on the bank.

What happens if I miss my payroll deadline?

You have a couple different options.  You can:

• Run an off cycle payroll and select a new paydate that would allow direct deposits to occur 
• Run the normal payroll with live checks only 

How do I run an off-cycle payroll?

1. Go to Payroll > Off-Cycle Payroll.
2. Answer required questions.
3. Click Next and process payroll.

Do I get charged for extra payroll runs?

No, Homebase does not charge per payroll run.  Your payroll fees are based on a flat amount + the number of employees you paid in a month (not the number of payrolls).  

Can I run payroll on multiple pay frequencies (e.g., weekly & bi-weekly)?

No, you must choose one pay frequency for all employees.  Caveat:  If you have more than one Federal ID / Homebase account, you can setup a different pay frequency on each company/account.  

How do I pay my employees a flat amount?

Enter the flat amount in the "Additional Earnings" field.

How do I pay and record holiday pay?

See details on Holiday Pay Rates.

Why can’t I edit hours directly in payroll?

Payroll pulls hours from Timesheets.  If you need to adjust the amount of hours an employee is paid, you must adjust their timesheet prior to starting payroll.  If you already started payroll, you will want to delete the draft, update the timesheet, then re-start payroll. 

Can I process multiple rates on an off-cycle payroll?

• Yes, but only if different rates are pulled from Timesheets. 
• If you do not have different rates / roles on a timesheet for an employee (or if you are manually keying hours in an off cycle), you will not be able to have multiple rates on the off-cycle.  

Why does the wage rate show ‘dashes’ in payroll?

Possible reasons:

• No wage rate entered in Job Details.
• Incorrect effective date for wage rate.

Why can’t I edit an employee’s pay rate in payroll?

Pay rates must be updated in the employee’s Job Details section before running payroll.

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PTO, Holiday Pay, and Time Tracking

How do I set up PTO for employees?

See this guide.

Why wasn’t PTO applied to an employee’s paycheck?

• Verify that the employee is assigned to a PTO policy
• Ensure PTO was requested by the employee

How do I pay time and a half for holiday work?

See Holiday Pay Rates.

How do cash/credit tips work?

See Tracking Cash & Credit Tips.

Can I add deductions for contractors?

No, Homebase does not support deductions for 1099 contractors.

How does Tip Manager work?

Tip Manager allows you to set up tip pooling and distribution policies.  The most common being where you enter a pooled tip amount for the week and then the tip manager will proportionately distribute tips to employees based on the amount of hours worked. 

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Homebase Integrations & Reports

How do I export payroll data to QuickBooks?

See QuickBooks Integration Guide.

How do I set up QuickBooks Chart of Accounts?

Follow this guide.

Where can I find my Washington L&I Rates?

1. Visit Washington L&I Rates.
2. Select Search by WA UBI.

What Homebase plan am I on, and what features do I have?

You can review and update your Homebase plan in account settings.