This article is about Justworks Payroll. What product am I using?
As your payroll provider, Justworks Payroll will submit payroll tax filings to the IRS on behalf of your company for the year. In order for us to submit these tax filings on time and correctly, we’ll need you to complete the End of Year tasks outlined below prior to the IRS’ deadlines.
1. Verify Employee Information
Make sure employee details are accurate. This helps prevent errors and reduces the chance of tax document corrections later. We’ll remind employees to review their own information too, but a direct ask from you goes a long way.
How to review employee information:
For you (as an admin):
Go to the Company Census in your Analytics tab and verify each employee’s:
- Full name
- Home and work address
- SSN
For your employees:
Ask them to review their information in their Profile (under You), including:
- Full name
- SSN
- Mailing address
- Tax withholdings and allowances
- Year-end form delivery method
Note: Changes to withholdings only apply moving forward. Employees should verify their details now to avoid potential tax issues from underwithholding.
2. Remind employees to use FSA funds
Unlike Health Savings Accounts (HSAs), which roll over year to year, most Flexible Spending Accounts (FSAs) expire at the end of the plan year. If you offer an external FSA, confirm the plan rules with your provider and share key deadlines with employees so they can use any remaining funds in time.
If you offer an FSA through Justworks Payroll:
- Healthcare FSA: Employees can roll over up to $640 into the new plan year.
- Dependent Care FSA: Funds must be used by December 31, 2025 — they won’t roll over.
- Claims: Expenses incurred in 2025 must be submitted by March 31, 2026.
3. Coordinate payroll with employees’ 401(k) contributions
To get the most from pre-tax contributions, employees may want to adjust their 401(k) rate for their base salary or bonus/commission pay before the final payrolls of the year. Talk with employees about their plans before scheduling any bonuses.
How updates can be made:
By you (if you use an external 401(k) provider):
- Edit employees’ manual deduction amounts in their profiles under Manual Deductions.
- If deductions should apply to specific payments, update the effective dates.
- After your company’s final payroll runs, change the deduction amount back so the higher rate doesn’t carry into the new year.
By your employees (if you use Guideline through Justworks Payroll):
- Employees must update contributions directly in Guideline.
- Remind them to make changes at least 5-6 business days before payroll is processed.
Important: Remind employees that, if they increase their contribution amounts to max out for 2025, they must change it back after your company's final payroll runs. Contribution rates don’t automatically reset in the new year.
4. Enter your company’s tax information
If you haven’t already, complete the “Manage your company tax information” task on your homepage. For Justworks Payroll to remit payments and file on your behalf, your company’s tax information must be on file. In some states, third-party administrator (TPA) access is also required.
If we don’t have the necessary tax information—and TPA access where applicable—Justworks Payroll won’t be able to complete your filings on time. In that case, your company would be responsible for any penalties or fees from late filings.
Note: If you do not see this task on your homepage, you’re all set.
How to submit your company’s tax information:
- On your Homepage, go to Your company tasks.
- Click Start in the Manage your company tax information.
- Review your company’s tax details.
- Update as needed and submit.
TPA Access: In many states, Justworks Payroll also needs TPA access to file and pay on your behalf. Once you submit your company’s tax information, we’ll initiate this process if your state requires it. Be on the lookout for an email from our support team with next steps, and complete them promptly to avoid delays.
5. Record employee payments made outside Justworks
All salary and one-time payments for employees must be recorded in Justworks Payroll. If you issued a payment outside of Justworks (like a physical check or direct wire), you’ll need to record it as an External payment in the Payments Center.
How to record an external payment:
- Go to the Payments Center.
- Set up an External payment for the employee.
- Enter the details of the payment (salary, bonus, commission, etc.).
Note: External payments follow the same processing timelines as regular payroll. Any 2025 external payments must be recorded before your company’s final processing date.
6. Record imputed income
Imputed income is the value of non-wage compensation that is considered taxable for your employees.
Examples of taxable imputed income:
- Taxable fringe benefits: extra perks like a vehicle, gym membership, or other non-cash benefits
- Taxable equity-based compensation: non-cash pay tied to company stock, such as options or restricted stock
If you’re unsure of whether a benefit or perk is taxable, you should consult with the benefit’s provider or your company’s tax advisor.
How to record imputed income:
- Go to Payments Center > Record Payments.
- Select Imputed income and record per employee, as applicable.
- Choose a pay day in 2025 to ensure the income and associated taxes are applied correctly.
Reminder: Applicable taxes will be withheld. If recording a large amount, consider the impact on their usual paycheck to avoid errors or a low net payment
7. Report employer contributions to outside health benefits
We need to know whether your company made contributions to any of the following benefits outside of Justworks Payroll during 2025:
- Medical Insurance
- Dental Insurance
- Vision Insurance
- Health Savings Account (HSA)
Important: Reporting these contributions now ensures they’re included accurately on tax filings
How to report employer contributions:
- Navigate to the End of Year Task List in your Justworks Payroll account and download our Excel template
- For each applicable employee, enter contribution amounts for any outside medical, dental, vision, or HSA benefits.
- Save your completed file as a .csv.
- Email the file to support@payroll.justworks.com
8. Review your final payroll
Make sure all payees and amounts listed for your final payroll of the year are correct, especially if you prorated any payments.
How to review final payroll:
- Go to your Dashboard > Upcoming Payments.
- Click View estimate next to your final payroll date.
- Review the details to ensure everything is scheduled correctly.
9. Schedule all one-time payments
To be included on 2025 Forms W-2 or 1099, payments must be issued to recipients in 2025 by your final payroll processing date. Make sure to enter all 2025 payments prior to this deadline.
How to schedule final payments:
- Go to the Payments Center.
- Schedule all remaining 2025 payments (such as bonuses, commissions, owners’ draws, etc.) by your final payroll processing date.
Reminder: Payments scheduled after your company’s final processing day will be issued in 2026 and included in 2026 tax filings.
10. Review and update state tax details for 2026
At the start of each year, many state tax departments assign updated tax rates or deposit schedules. Keep an eye out for mail from the state(s) where your company is registered.
If you receive updated state tax account details, submit the new information in Justworks Payroll after your final processing date of 2025:
- Expand Company Settings in the left-side menu and click Compliance.
- Click on Company taxes.
- Select the state with updated information.
- Click Edit and save your changes.
Disclaimer
This material has been prepared for informational purposes only, and is not intended to provide, and should not be relied on for, legal or tax advice. If you have any legal or tax questions regarding this content or related issues, then you should consult with your professional legal or tax advisor.