Payroll with Homebase - Common FAQs

This guide provides answers to common payroll implementation questions. If you need further assistance, visit our Help Center or reach out to support.

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Payroll Processing & Payment Speed

Why am I on 3-day processing instead of 2-day?

Eligibility requirements determine processing speed. Learn more here.

If I have insufficient funds (NSF) and request a wire, when will my employees be paid?

After Homebase receives the wire transfer, typically within 24 hours of receiving the funds.

How do I run a late payroll?

Click the Late Payroll button on the Payroll Dashboard. You will have the option to issue paper checks for the same pay date or direct deposit for the next available deposit date.

Can I ignore the payroll schedule and run all off-cycle payrolls?

Yes, Homebase allows you to run off-cycle payrolls as needed. Learn more: Off-Cycle Payroll.

How much does it cost to run an off-cycle payroll?

There is no additional charge—you can run as many off-cycle payrolls as necessary.

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State Tax IDs & Compliance

Can Homebase help me get my state tax ID?

Homebase cannot register for your tax ID, but you can find steps and links for registration here.

What is a SOC code, and how can I get it?

SOC (Standard Occupational Classification) codes are issued by the U.S. Department of Labor. Find more details:

• Washington Registration
• Louisiana Registration

How do I find my Washington L&I rate?

Follow these steps:

1. Go to Washington L&I Verification.
2. Search by WA UBI.
3. Click on the company name.
4. Scroll to “Workers Comp” and click “View Rates.”

How do local taxes work in Homebase?

Local taxes may be employer- or employee-paid, depending on the locality. More details here.

Why are local taxes appearing on my employees when they shouldn't be?  

If locals are appearing on your payroll when they shouldn’t be, it could be due to several reasons-

Multi-Location Employee Issues: Employees assigned to multiple locations might not have all their workplaces correctly reflected in payroll processing. This can cause discrepancies if their company ID or workplace assignments are not updated properly

Local Tax Withholding Errors: Incorrect local tax settings might cause employees to appear incorrectly on payroll. Ensuring that local tax settings are correctly configured can help resolve these issues

Local Tax Reporting: Payroll systems report to the workplace locality where the employee physically works. The higher tax rate between the workplace and home locality is used to ensure compliance. This means that even if an employee lives in a different locality, the workplace tax might be applied, causing locals to appear on payroll

These issues can often be resolved by reviewing employee profiles, ensuring correct workplace assignments, and verifying payroll settings.

How do I set up Third-Party Administrator (TPA) access?

Refer to our State-by-State TPA Setup Guide.

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Year-to-Date (YTD) Payroll Information

Why do I need to provide YTD payroll history?

YTD data ensures:

• Accurate tax filings and reporting.
• Employee paychecks reflect correct year-to-date earnings and deductions.
• Proper W-2 reporting at year-end (only one payroll provider can file W-2s per year).

Can I submit a total YTD amount instead of payroll-by-payroll details?

No, we require payroll period data to balance taxes and avoid discrepancies. However, for closed quarters, we can accept a payroll summary. For both closed and open quarters, tax breakdowns per employee are required (Federal Income Tax, State Income Tax, Federal Unemployment, State Unemployment, Social Security, Medicare).

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Employee Payroll Setup & Tax Filings

What is required to pay an employee?

See our guide: How to Add an Employee to Payroll.

Does Homebase file quarterly taxes and deposits?

Yes. Learn more about tax filings:

• Federal & State Payroll Tax Forms
• View Tax Payments & Returns

Will my SUI rate update automatically?

No. You’ll receive a letter from your state annually. Update it in Settings > Taxes.

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Payroll Processing & Paychecks

How do I print paper checks?

Note: See Printing Paper Paychecks.

How do paper checks work in Homebase?

• Homebase does not mail checks.
• Taxes are collected, and net pay is calculated.
• After submitting payroll, you can print checks using pre-printed check stock.
• Order check stock (Layout DLT159) here.

When will my payroll funds be withdrawn?

• Funds are collected same day or next business day after payroll submission.
• Ensure funds are available at the time of payroll processing.

How do I fund payroll via wire transactions?

To fund your payroll by wire due to an NSF see Resolve a Bank Error on Payroll or if you need to set up a one time fund by wire payroll see Fund by Wire. 

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Salaried Employees & Payroll Settings

How do I set up employee salaries?

1. Go to Employee Profile > Access, Wages & Roles.
2. Click Edit and update wage type to Annual Salary.
3. Enter the annual salary amount to be paid.  Homebase will calculate per-pay-period amounts.

How do I handle salaries for multi-location employees?

• If an employee is paid under one location but works at multiple, enter the salary only under that location.
• If they are paid from multiple locations, divide the total salary by the number of locations and enter it accordingly.  You will also need to do this with the hours.  

How do I calculate annual salaries?

Use our guide: How to Calculate Annual Income.

Will my employees’ pay rates update automatically for minimum wage changes?

No, you must manually update wages in each employee’s profile.

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Payroll Software Integrations

How do I export payroll data to my Accounting software?

• QuickBooks Online Plus Integration Guide
• Export Payroll Data to Accounting Software

How do I set up my QuickBooks Chart of Accounts?

• QuickBooks Chart of Accounts Setup

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Paid Time Off (PTO) & Employee Notifications

How do I set up PTO policies?

• PTO & Paid Sick Leave Guide

Will new hires automatically be added to PTO policies?

No, you must manually add them to the policy.

Will my holiday settings update annually?

No, update them manually in Settings > Overtime > Holiday Pay Rates.

Can I turn off pay stub email notifications for employees?

No, all employees receive an automated payday email with a pay stub link.

Why can't I enter PTO on an employee? 

• Please review the following items below-  
• Missing Duration Information: There might be an issue where the system requires the “Days durations duration in minutes” field to be filled. If this field is left blank, it can prevent PTO from being added. To resolve this, ensure that all required fields, including duration in minutes, are completed when entering PTO.
• Policy Assignment: Make sure that the employee is assigned to a PTO policy. Without being assigned to a policy, PTO cannot be applied to the employee
• Plan Limitations: If you are on a specific Homebase plan, ensure that your plan allows for the creation and management of PTO policies. Some features might be restricted based on the plan you are subscribed to
• Technical Issues: If there are technical issues, such as problems with the mobile app, try troubleshooting steps like signing out, uninstalling and reinstalling the app, and clearing the cache and cookies to see if that resolves the issue

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New Hire & Payroll Setup Issues

Does the W-4 form automatically update employee profiles?

• Yes, if completed electronically in Homebase.
• No, if completed on paper—you must manually enter the data.

Why are documents missing from my previous payroll provider?

We import payroll history reports, but not individual documents from previous providers.

My employee hasn’t received the new hire paperwork link. What should I do?

• Verify their email is correct.
• Have them check their spam/junk folder.
• Resend the invite from their profile in Homebase.

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I’m trying to finish setting up payroll, but it won’t let me submit it for review. How can I fix this?

If you are experiencing issues or delays while setting up payroll, please reach out to your Implementation Specialist to understand the next steps.

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Other Payroll-Related Questions

Are my children or employees exempt from taxes?

Tax exemption rules vary. Consult with a tax professional or your state’s tax agency.

How does the 2% shareholder rule work?

This rule applies to S-corporation shareholders. Consult with a payroll specialist for compliance guidance.  You can also review This Article

Do child support payments get remitted?

Yes, Homebase Payroll supports child support garnishment payments.

Do you withdraw for benefits/deductions during payroll?

Yes, but Homebase does not send payments directly to benefit providers except for state-mandated child support garnishments.

When can I apply for Stride health insurance?

You can apply anytime. More info: Stride Health FAQs.

How does Cashout work?

• Cash Out

Why do some employees have the 2% shareholder field while others don’t?

This field does not appear for:

• 1099 contractors
• Employees with incomplete payroll profiles

Can I use an ITIN (Individual Taxpayer Identification Number) for my employees

Yes, but only for contractors (individuals or businesses). ITINs cannot be used for W-2 employees.

How do I enter a reimbursement?

Enable the "Reimbursements" column in payroll processing.

How do I enter an amount for gifts given to employees?

Categorize gifts under "Other Imputed Income".

Can I pay an owner's draw?

Yes, but it must be entered as a reimbursement.

How do I cancel pending team member invites?

Pending invites cannot be canceled directly. Contact Homebase Support for assistance.

Do I need a paid plan to use Homebase Payroll?

No, Homebase payroll is an add-on that can be purchased at any tier. 

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What does "Company start date must be in the future" mean?

This error can appear when you try to submit your first payroll run after your implementation start date has already passed. The company start date is the date set during implementation to mark when you will begin running payroll in Homebase.

Note: This error only occurs before you run your first payroll. Once your account is fully live, you should not encounter this message again.

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Does Homebase report time tracking Electronic Visit Verification (EVV)?

An Electronic Visit Verification (EVV) system electronically verifies that Medicaid-funded home and community-based services, such as personal care and home health, occurred by recording the service type, client, caregiver, location, and exact start and end times of a visit.

Homebase does not support reporting to EVV.