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 by your company’s final off-cycle processing date.
How does the End of Year task list work?
The End of Year task list in Justworks Payroll guides admins through the actions and information needed for a successful year-end. Complete the tasks that apply to your company, and Justworks handles the filing from there.
How do I find the task list?
Go to Home and select Get started on the End of Year banner. The task list stays on Home until the deadline.
When are tasks due?
All tasks are due by your company’s final off-cycle processing date, shown at the top of the task list. Every task has the same recommended completion date, so you can work through them in any order and finish by that date.
Which tasks are required?
Each task shows a task type. Required tasks apply to every company and can’t be skipped. As applicable tasks depend on your company, so complete the ones that apply and skip the rest.
How do I mark tasks as done?
Check off each task when you complete it. If a task doesn’t apply to your company, select Skip to keep your list clean and organized.
Do multiple admins share the task list?
Yes. All admins share the same task list, so changes are reflected for everyone.
What does Justworks file for my company?
Once you’ve finished your tasks, Justworks files the following for your U.S.-based employees and contractors, as applicable:
- Forms W-2
- Forms 1099-NEC
- Form 940 (Federal Unemployment Tax Return)
- Form 941 (Quarterly Federal Tax Return)
- State and local payroll tax returns
1. Verify employee information
Make sure employee details are accurate to prevent errors and reduce 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.
For you:
- Go to your Company census and verify each employee’s:
- Full name
- Address
- SSN
- Office location
- If you have employees on tax-exempt visas, go to People and verify their exemptions are recorded in the Tax information tab of their profile.
- Go to Company details and verify all office addresses are correct.
For your employees:
Ask them to review their Profile information, including:
- Full name
- SSN
- Mailing address
- Tax info in Finances
- Year-end form delivery method in Finances
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.
For FSAs offered through Justworks Payroll:
- Healthcare FSA: Employees can roll over up to $680 into the new plan year.
- Dependent Care FSA: Funds don’t roll over, and must be used by December 31, 2026.
- Claims: Expenses incurred in 2026 must be submitted by March 31, 2027.
3. Coordinate payroll with employees’ 401(k) contributions
Before you send any bonuses or run your final payroll, you can help employees make the most of their 401(k). Talk with them about maximizing pre-tax contributions by increasing their 401(k) rate for salary or bonus/commission pay.
If you integrate with Vestwell:
- Employees update contributions directly in Vestwell.
- Remind them to make changes at least 2 business days before payroll is processed.
Important: Remind employees that if they increase their contribution amounts to max out for 2026, they must change it back after your company's final payroll runs. Contribution rates don’t automatically reset in the new year.
If you use an external 401(k) provider:
- Edit employees’ manual deduction amounts in their profiles under 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.
4. Check your company’s tax information
We need complete company tax information to make payments and file on your behalf. Missing information can delay filings and may result in penalties or fees for your company.
How to check your company’s tax information:
- Go to Company settings > Compliance.
- Under Company taxes, look for any states marked Incomplete.
- If you see Incomplete, select that state and provide the missing information.
- No Incomplete badges? You’re all set!
Third-party administrator (TPA) access: In many states, we also need TPA access to file and pay on your behalf. If required, our support team will email you with next steps after you submit your tax information. Complete those steps promptly to avoid filing or payment delays.
5. Record employee payments made outside Justworks
If you issued any payments to employees outside of Justworks (like a physical check or direct wire), they’ll need to be recorded as an External payment.
How to record an external payment:
- Go to Pay > Make a payment.
- Find the payment type you need to record, and select External payment under Payment method.
- Enter the details of the payment.
If you made any contractor payments, please contact us to record them. Reach out to customer support at (646) 681-7473 or support@payroll.justworks.com.
Note: External payments follow the same processing timelines as regular payroll. Any 2026 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:
- 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, consult your tax advisor or the benefit provider.
How to record imputed income:
- Go to Pay > Make a payment and select Record Payments.
- Select Imputed income and record per employee.
- Choose a pay date in 2026 to ensure the income and associated taxes are applied correctly.
Reminder: Applicable taxes will be withheld. Consider the impact on an employee’s usual paycheck to avoid errors or a low net payment.
7. Report >2% S-Corp shareholders
If your company is an S-Corp, make sure all shareholders who own more than 2% are correctly identified and any applicable imputed income is recorded. Imputed income is the value of certain non-cash benefits, such as health insurance premiums paid on behalf of >2% S-Corp shareholders.
How to do it
- Go to Company settings > Profile > Edit details and verify Tax classification is marked as S corporation.
- Go to your Company census and verify the right people are marked as owners. To add or edit an owner, go to the individual’s profile, select Schedule job change, and update their Profile type to Paid owner.
- If you add or edit an owner, contact Customer Support to review possible tax implications of the change.
- To record any shareholder imputed income, go to Pay > Make a payment and select Record Payments.
8. Report employer contributions to outside health benefits
What to report:
You only need to report the employer contributions for health benefits administered outside of Justworks Payroll:
- Medical Insurance
- Dental Insurance
- Vision Insurance
- Health Savings Account (HSA)
Don’t report:
- Employee contributions
- COBRA payments
- CHOICE (formerly ICHRA) contributions
- Premiums for benefits administered through Justworks
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
9. Review 1099 information for U.S.-based contractors
Review your Payroll Detail Report to confirm the 2026 payment and filing information we have for your U.S.-based contractors. Confirm that:
- All contractor payments are included, including any payments made outside of Justworks.
- Payment amounts are accurate.
- Justworks should file Forms 1099 for the contractors shown.
Need to make a change?
Update missing or incorrect information for contractors in their profile. Contact Customer Support at (646) 681-7473 or support@payroll.justworks.com if:
- A payment made outside of Justworks needs to be added or corrected.
- You do not want Justworks to file a Form 1099.
Make sure account setup is complete: We can only issue Forms 1099 for contractors who complete their account setup by the deadline. Follow up with anyone who has missing or incomplete information.
10. Review federal overtime hours
Review federal overtime hours for non-exempt employees to make sure amounts are accurate. Federal overtime is time worked beyond 40 hours in a workweek and paid at 1.5x the employee’s regular rate. For 2026, federal overtime information is reported on employees’ Forms W-2.
How to review overtime reported so far:
- Go to Analytics > Reports, open the FLSA overtime report, and review each non-exempt employee’s overtime by workweek.
- The report includes data through your most recent pay period. Return any time to review the latest data.
- If anything looks incorrect, download the report as a CSV, make your changes in the file, and email it to support@payroll.justworks.com. Request corrections before your company’s final off-cycle processing date. Changes requested after that date require a Form W-2c.
Overtime you schedule manually under Other supplemental pay isn’t included automatically. To include these amounts, add them through the CSV correction process above.
Keep overtime accurate for remaining payrolls: Make sure hours are entered correctly for each remaining pay period. For more about how overtime is calculated and reported, see FLSA overtime reporting.
11. 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 Home to see your Upcoming Payments.
- Select View estimate next to your final payroll date.
- Review the details to ensure everything is scheduled correctly.
12. Schedule all one-time payments
Any payments that need to be included on 2026 Forms W-2 or 1099 must be issued to recipients in 2026. The last day your company can process 2026 payments is your company’s final off-cycle processing date.
How to schedule final payments:
- Go to Pay > Make a payment.
- Schedule all remaining 2026 payments (such as bonuses, commissions, owners’ draws, etc.) by your company’s final off-cycle processing date.
Reminder: Payments scheduled after your company’s final processing day will be issued in 2027 and included in 2027 tax filings.
13. Review state tax details for 2027
At the start of each year, many state tax departments assign updated tax rates or deposit schedules. If you receive updated state tax account details for 2027, submit the new information after your final processing date of 2026:
- Go to Company settings > Compliance.
- Pick the state to be updated.
- Select Edit to make any changes and then Submit 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.