Missouri LLC taxes depend on how the IRS classifies your business. Most Missouri LLCs are pass-through entities, so the LLC itself owes no income tax; instead, profits flow to the owners, who pay Missouri individual income tax at rates up to 4.7 percent for 2026. On top of that, you may owe federal self-employment tax, state and local sales tax, payroll taxes if you have employees, a 1 percent earnings tax in St. Louis or Kansas City, and county personal property tax on business equipment.
How Your Federal Tax Classification Decides What You Owe
Missouri law requires every LLC to be taxed the same way it’s classified for federal purposes.1Missouri Revisor of Statutes. Missouri Code 347.187 – Classification for Purposes of Taxation — Treatment You never make a separate state election. Whatever the IRS says you are, that’s what Missouri treats you as.
There are four possibilities:
- A single-member LLC is a disregarded entity by default. You report business income and expenses on Schedule C of your personal Form 1040 and carry the same number onto Missouri Form MO-1040.2Internal Revenue Service. About Schedule C (Form 1040)
- A multi-member LLC is a partnership by default. The LLC files federal Form 1065 and Missouri Form MO-1065 for information only, and each owner gets a Schedule K-1 showing their share of the profit to report on their individual return.
- Any LLC can elect S-Corporation treatment by filing IRS Form 2553. The LLC files Form 1120-S federally and MO-1120S in Missouri, and profits still pass through to owners on K-1s.
- An LLC can elect C-Corporation treatment by filing IRS Form 8832. Now the LLC is a separate taxpayer, pays corporate tax on its profits, and owners are taxed again on any dividends.
Three of these four options mean the LLC itself writes no income tax check. Only the C-Corporation election creates entity-level income tax.
Income Tax on Your Share of the Profits
If your LLC is a disregarded entity, partnership, or S-Corporation, you pay Missouri individual income tax on your share of the profits. The state uses a graduated rate structure, with the top rate of 4.7 percent kicking in on taxable income above roughly $9,400 for 2026.3Missouri Department of Revenue. 2026 Missouri Withholding Tax Formula The rate has been dropping in recent years and may fall further if state revenue triggers are met.4Missouri Revisor of Statutes. Missouri Code 143.011 – Tax Imposed — Rates
Single-member owners report business income directly on Form MO-1040. Partners and S-Corporation shareholders use the K-1 their LLC issues to fill in the business income section of their own MO-1040. Either way, the tax is paid on the individual return.
Quarterly Estimated Payments
If you expect to owe at least $100 in Missouri income tax for the year, you have to make quarterly estimated payments using Form MO-1040ES.5Missouri Department of Revenue. MO-1040ES – Declaration of Estimated Tax for Individuals This catches almost every LLC owner with real income, because nothing is being withheld from pass-through profits. The deadlines mirror the federal schedule: April 15, June 15, September 15, and January 15 of the following year.
When the LLC Itself Pays Income Tax
Two scenarios put the tax bill on the LLC rather than the owners.
The first is a C-Corporation election. A Missouri LLC taxed as a C-Corp files Form MO-1120 and pays a flat 4 percent on its Missouri taxable income.6Missouri Revisor of Statutes. Missouri Code 143.071 – Corporation Income Tax Rate Owners then pay personal tax again on any dividends they take out. That double layer is why most small LLCs avoid the C-Corp route.
The second is the optional pass-through entity tax (PTE tax), available to LLCs classified as partnerships or S-Corporations. The LLC elects it each year on Form MO-PTE and pays Missouri income tax at the top individual rate at the entity level; owners then claim a credit on their personal return for the tax the entity paid.7Missouri Department of Revenue. Form MO-PTE Instructions8Missouri Revisor of Statutes. Missouri Code 143.436 – Pass-Through Entity Tax The point of the election is to work around the $10,000 federal cap on state and local tax deductions by routing the state tax through the business as a deductible expense. It helps owners who already max out the SALT cap and itemize; for others, it changes nothing.
Missouri does not charge an annual franchise tax on LLCs.
Federal Self-Employment Tax
This is the one that catches new LLC owners off guard. If your LLC is a disregarded entity or partnership, your share of the profit is subject to federal self-employment tax of 15.3 percent on top of regular income tax.9Internal Revenue Service. Self-Employment Tax (Social Security and Medicare Taxes) That’s 12.4 percent for Social Security on the first $184,500 of net self-employment income in 202610Social Security Administration. Contribution and Benefit Base and 2.9 percent for Medicare with no cap. An additional 0.9 percent Medicare surtax applies above $200,000 for single filers or $250,000 for joint filers.
This is the main reason some owners elect S-Corporation treatment. With an S-Corp, only the wages you pay yourself are hit with payroll taxes; profits distributed on top of that salary are not. The trade-off is running real payroll, filing employment returns, and paying yourself a salary the IRS considers reasonable for the work you do. For smaller operations, the compliance cost can eat the savings.
Sales and Use Tax
If your LLC sells tangible goods or certain taxable services in Missouri, you need a sales tax license from the Department of Revenue and you have to collect tax from customers. The state rate is 4.225 percent, but cities, counties, and special districts stack their own rates on top, pushing combined rates past 10 percent in some areas.11Missouri Department of Revenue. Sales and Use Tax You need to look up the correct rate for every location where you make sales.
Collected tax goes to the DOR on Form 53-1. Filing frequency (monthly, quarterly, or annually) depends on volume. Even a zero-sales period still requires a return.
Use tax is the mirror image. When your LLC buys equipment or supplies from an out-of-state vendor that didn’t charge Missouri sales tax, you owe use tax at the same combined rate. It’s easy to overlook and the DOR treats underreporting of it seriously.
Resale Exemption Certificates
Inventory you plan to resell is not supposed to be taxed at the wholesale stage. You give the seller a completed Form 149 along with your Missouri retail sales tax ID, and they treat the sale as exempt.12Missouri Department of Revenue. Sales and Use Tax Exemption Certificate You then charge sales tax to the end customer. Using a resale certificate to buy things for personal use creates problems with the DOR fast.
Payroll Taxes If You Hire Employees
Hiring triggers two state obligations beyond the usual federal payroll taxes.
The first is state income tax withholding. Register for a withholding account with the DOR, deduct Missouri income tax from each paycheck, and remit it on Form MO-941.13Legal Information Institute. 12 CSR 10-2.015 – Withholding of Tax Filing frequency scales with payroll size.
The second is state unemployment insurance. You pay SUI tax on each employee’s wages up to a $9,000 taxable wage base for 2026, down from $9,500 in 2025. New employers in most industries start at 2.376 percent for 2026; 501(c)(3) nonprofits start at 1.0 percent.14Missouri Department of Labor and Industrial Relations. Tax Rates Your rate moves up or down over time based on your experience with unemployment claims.
Local Earnings Tax in St. Louis and Kansas City
Two Missouri cities charge their own earnings tax on top of state and federal taxes: St. Louis and Kansas City. Both impose a flat 1 percent tax on the net profits of businesses operating inside city limits and on wages earned there.15City of St. Louis. Business Earnings Tax Information16City of Kansas City. Have You Paid Your KCMO Earnings Tax (E-Tax)?
If your LLC is located in either city or performs work there, you file a local return and pay 1 percent of net profit. Non-resident businesses that perform services inside city limits owe it too. If you have employees working in either city, you also withhold the 1 percent from their wages and remit it to the city. Nonprofits with a federal or state tax-exempt certificate are generally exempt.15City of St. Louis. Business Earnings Tax Information
LLCs outside those two cities don’t owe this tax.
County Personal Property Tax on Business Assets
Missouri taxes tangible personal property used in business, including equipment, vehicles, furniture, computers, signage, and supplies. Each year the county assessor mails a Business Personal Property Assessment form, and you have to complete and return it by March 1. The assessed value drives a property tax bill set by your county and any overlapping taxing districts.
This isn’t a state tax, so the rate and bill come from your county. But every Missouri LLC that owns or controls business assets has to file the assessment form, and missing the March 1 deadline triggers penalties.
Penalties, Interest, and Annual Upkeep
Missouri charges 7 percent annual interest on underpaid or late-paid tax for 2026, accruing daily on the unpaid tax balance.17Missouri Department of Revenue. Statutory Interest Rates
Sales tax penalties show how quickly late filings pile up. Filing on time but paying late is a one-time 5 percent penalty on the unpaid amount. Failing to file at all is 5 percent per month, capped at 25 percent, plus the 7 percent annual interest on top.18Missouri Department of Revenue. Maintain Sales/Use Tax The DOR treats collected sales tax as money held in trust for the state, and the enforcement reflects that.
On the administrative side, Missouri is unusually light. Domestic LLCs don’t file an annual report or pay a yearly fee to the Secretary of State to stay in good standing.19Missouri Secretary of State. General Services and Filings You pay a one-time filing fee at formation and then just need to keep a current registered agent and business address on file. Some cities require a local business license with its own renewal, so check with your municipality, but the state itself asks almost nothing of an active LLC year to year.