Why Payroll Compliance Is a Bigger Deal Than You Think
Running payroll isn’t just about issuing checks—it’s about complying with a complex system of employment, tax, and immigration rules. Many small business owners unknowingly expose themselves to penalties, audits, and even personal liability by overlooking key payroll requirements.
If you’re paying employees, hiring contractors, or drawing income as an S-corp owner, payroll compliance should be high on your radar.
What Is Payroll Compliance?
Payroll compliance means following all federal, state, and local laws when it comes to:
Verifying that employees are legally eligible to work
Classifying workers properly as employees or independent contractors
Withholding and remitting payroll taxes
Filing payroll tax forms on time
Paying S-corporation owners a reasonable wage
Complying with wage, hour, and benefit laws
I-9 Compliance & E-Verify
Every employer must complete Form I-9 for each new employee to verify identity and work eligibility. This form must be completed within three business days of hire and kept on file for specific retention periods.
In addition to the I-9, some states require or allow employers to use E-Verify, an online system that cross-checks information with federal databases to confirm work authorization.
In Florida, E-Verify is now mandatory for private employers with 25 or more employees.
Failure to comply can lead to significant fines, business license suspension, and audits by immigration authorities.
Knowingly hiring someone who isn’t authorized to work in the U.S. can also result in criminal penalties.
Misclassifying Employees as Contractors
Misclassifying an employee as a 1099 contractor is a common payroll mistake with serious consequences.
Employees are entitled to benefits such as unemployment insurance, workers’ compensation, and tax withholding. Contractors are not.
Government agencies look at factors such as:
Who controls how the work is done
Whether the worker is financially dependent on the business
The permanency of the relationship
Misclassification can result in back taxes, penalties, and liability for unpaid benefits.
Payroll Tax Filing Requirements
If you have employees, you are responsible for:
Withholding federal income tax, Social Security, and Medicare from each paycheck
Paying the employer portion of Social Security and Medicare
Depositing payroll taxes on a regular schedule
Filing tax returns, such as quarterly payroll reports and annual unemployment tax forms
Issuing W-2s to employees and filing them with the Social Security Administration
Reporting new hires to the state
Late deposits or incorrect filings can lead to substantial penalties, including interest charges and per-employee fines.
Reasonable Compensation for S-Corporation Owners
If you're an owner of an S-corporation and you provide services to the business, you are considered an employee and must be paid a reasonable salary.
You must:
Pay yourself through payroll, not just take owner draws or distributions
Withhold and pay employment taxes on your wages
File the same payroll forms and year-end W-2s as you would for any other employee
One of the most common audit red flags for S-corporations is an owner who takes large distributions without taking a salary. This can trigger back tax assessments and penalties.
Other Common Payroll Pitfalls
Here are some of the most common payroll compliance issues we see:
Missing I-9 forms or failing to complete them on time
Paying employees “under the table” or in cash without proper reporting
Failing to report new hires to the state
Incorrectly issuing 1099s to employees who should receive W-2s
Missing payroll tax deposit deadlines
Incorrect PTO or sick leave tracking
Failing to follow state wage and hour laws on overtime, minimum wage, or pay frequency
Best Practices for Staying Compliant
Use a reliable payroll system or CPA to handle filings, tax deposits, and reporting
Complete I-9s and run E-Verify checks at the time of hire
Regularly review your workers’ classifications
Make sure S-corp owners on payroll are paid appropriately
Perform quarterly payroll reconciliations
Stay current with changing state and federal laws
Final Thoughts
Payroll compliance is not optional. Fines, interest, and tax liabilities can build quickly—and in some cases, owners can be held personally responsible. Whether you’re hiring your first employee or managing a growing team, proper payroll administration is essential to protecting your business.
Need help with payroll compliance, W-2s, or officer compensation?
We offer full-service payroll administration, compliance checks, and penalty resolution.
📞 Contact us today to set up a consultation and ensure your payroll process is fully compliant.