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Top Payroll Errors and How to Avoid Them

Top Payroll Errors and How to Avoid Them

A small oversight can lead to steep penalties, employee dissatisfaction, or even IRS scrutiny.

Read time

3 minutes

Written by

CFC Team

checkmark Understand both federal and state payroll laws to avoid penalties.
checkmark Keep accurate and secure records to prepare for audits and tax filings.
checkmark Automate processes and consider outsourcing for long-term peace of mind.

Key Differences at a Glance

CategoryLLCS-Corporation
TaxationPass-through by default; can elect S-CorpPass-through only; subject to eligibility
Owner EmploymentMembers are not employeesShareholders must pay themselves reasonable salary
Self-Employment TaxFull profits subject to SE taxOnly salary subject to SE tax
Ownership LimitsNo limit on number/type of members100 shareholder max; must be U.S. persons
FormalitiesFewer ongoing requirementsMore formalities and stricter rules

What is an LLC?

A Limited Liability Company (LLC) is a flexible business structure designed to protect its owners (called members) from personal liability while maintaining simplified tax and operational flexibility.

  • Pass-through taxation by default

  • Easy to form in all 50 states

  • Less paperwork and fewer maintenance formalities than corporations

What is an S-Corporation?

An S-Corporation (S-Corp) is not a business entity itself, but a special tax classification available to LLCs or corporations that meet IRS criteria. It allows the business to avoid double taxation by passing income directly to shareholders.

  • Owners must be U.S. citizens or residents

  • Limited to 100 shareholders

  • Must pay shareholder-employees a reasonable salary

Federal Tax Treatment

By default, an LLC is treated as a sole proprietorship (if single-member) or a partnership (if multi-member). Income is reported on the member’s individual tax return, and all profits are subject to self-employment taxes (Social Security + Medicare).

An S-Corp avoids self-employment tax on profits above the owner’s salary. However, the IRS requires that shareholders who work for the business must be paid a “reasonable” salary, which is subject to payroll taxes.

This can save thousands in taxes but requires more admin, including filing Form 1120-S and issuing W-2s.

Payroll and Owner Compensation

LLC members are considered self-employed and take draws—not wages. They don’t receive W-2s and must pay self-employment tax on their share of the income.

S-Corp owners who work in the business must be employees and take a reasonable salary (reported on W-2), with the remaining profit passed through as distributions not subject to self-employment tax.

Eligibility and Ownership Rules

LLCs have flexible ownership rules—they can have unlimited members, including other companies and foreign individuals.

S-Corps, on the other hand, are restricted to:

  • No more than 100 shareholders

  • Shareholders must be U.S. citizens or residents

  • No partnerships or corporations as owners

  • Only one class of stock allowed

Administrative Burden and Paperwork

LLCs have fewer administrative requirements. They typically need an annual report and operating agreement but no formal board meetings or resolutions.

S-Corps must maintain more corporate formalities, including:

  • Annual shareholder meetings

  • Board of directors and meeting minutes

  • Formal issuance of stock

Should You Elect S-Corp Status as an LLC?

If your LLC earns more than ~$40,000–$50,000 in net profit annually, electing S-Corp status could reduce self-employment taxes. But you must factor in additional payroll costs, bookkeeping, and compliance needs.

Tax Comparison Example

Based on $100,000 Net Profit

LLC (Default) LLC with S-Corp Election
Net Profit $100,000 $100,000
Owner Salary N/A $50,000
Self-Employment Tax $15,300 $7,650
Payroll Admin Costs $0 $1,200
Estimated Tax Savings — ~$6,450

Final Thoughts: Choose What Supports Your Growth

LLCs offer flexibility, simplicity, and protection with minimal upkeep. S-Corps, while more complex, provide potential tax advantages that can support scaling up—especially once you’re consistently profitable.

Still unsure? Consulting a tax professional can help weigh short- and long-term pros and cons for your specific situation.

Why Outsourcing Entity Selection and Tax Planning Matters

Choosing the right entity structure—and maintaining its compliance—takes more than a quick form. Outsourcing this to experienced professionals ensures your tax elections, payroll setup, and filings are done correctly from the start.

This saves time, reduces audit risk, and positions your business to grow without surprises.

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