Payroll Missouri: Employer Tax and Software Guide

I build HR software for small businesses, and in any state I look first for the payroll rules an owner would rather learn before the first paycheck than from a state notice. This guide covers what Missouri requires, the two city taxes that catch employers in the metros, and how 10 payroll providers compare, with published rates modeled at 5, 15, and 50 employees.

Missouri looks like a cheap state to run payroll in, and on two measures it genuinely is. The top income tax rate is 4.7 percent, down from 4.95 percent in 2023 under a revenue-trigger schedule that allows further cuts when state revenue grows enough. And the unemployment wage base dropped to $9,000 for 2026, among the lowest in the country and close to the federal floor.

Three things complicate that picture. Kansas City and St. Louis each levy their own earnings tax, and St. Louis adds a separate tax that the employer pays. State law requires corporations to pay most employees at least twice a month, a statutory obligation rather than a scheduling preference. And the minimum wage reached $15.00 on January 1, 2026, higher than Pennsylvania, Virginia, or Nevada.

What Missouri actually requires from employers

Four obligations sit on top of federal payroll: withholding state income tax and filing it on the schedule the state assigns, unemployment insurance, the minimum wage, and new hire reporting. Two of them are genuinely light, while two are the reason people get this wrong.

State income tax withholding and Form MO W-4

Missouri uses eight graduated brackets running from zero up to 4.7 percent. Unusually, the same bracket thresholds apply to every filing status, and only the standard deduction changes.

The 2026 withholding formula published by the Department of Revenue starts the top rate at $9,436 of Missouri taxable income. That means most full-time employees reach 4.7 percent on the bulk of their wages, even though the brackets look graduated.

Two changes are worth catching. First, Form MO W-4 no longer uses numerical allowances at all: the calculation runs off filing status, which selects the standard deduction, and the employee can ask for additional or reduced withholding on top.

The second change is in the withholding formula itself. The federal tax deduction step that older versions carried has been gone since tax year 2019, so a payroll system still subtracting federal withholding before applying the Missouri brackets will produce the wrong number. Supplemental wages paid separately, such as a bonus, may be withheld at a flat 4.7 percent.

Unemployment insurance

Missouri unemployment insurance is paid entirely by the employer through the Division of Employment Security, with nothing withheld from employees. The wage base moved down rather than up for 2026, which is unusual enough to be worth flagging.

The direction of the change is the practical point. A payroll system carried over from 2025 without updating will keep collecting on $9,500 of wages and overpay at your assigned rate on an extra $500 per employee. Verify the figure rather than assuming it rolled forward.

Minimum wage

The Missouri minimum wage has been $15.00 per hour since January 1, 2026, up from $13.75, per the Division of Labor Standards.

Voters approved Proposition A in November 2024, and House Bill 567, signed July 10, 2025, kept the rate. The bill also removed the automatic inflation adjustment tied to the Consumer Price Index that would have started in 2027 and repealed the statewide paid sick leave mandate.

The tipped minimum is $7.50 with the employer covering any shortfall to $15.00. Retail and service businesses with gross annual income under $500,000 may fall outside the state rate, though federal minimum wage rules still apply.

New hire reporting

New and rehired employees must be reported to the Missouri new hire program within 20 days of hire, under RSMo 285.300. Most full-service payroll plans file the report automatically, while self-service tiers generally leave it to you.

Filing and remitting Missouri withholding

The Missouri Department of Revenue assigns each employer a filing frequency from what was actually withheld in earlier periods, and Form MO-941 is the return on every schedule. A return is due for every period even when nothing was withheld, which is where seasonal employers pick up non-filer notices.

Quarter-monthly is a payment schedule rather than a fourth return. The monthly MO-941 still gets filed, but at least 90 percent of the tax moves four times a month and the balance clears with that return.

Keeping that schedule current is your job. If your assigned frequency no longer matches what you are withholding, you have to tell the Department, because it will not catch the mismatch for you.

Two more details are worth getting right at setup. Missouri lets timely filers keep part of the tax they withheld as a compensation deduction: 2 percent of the first $5,000 of tax withheld in a year, 1 percent on the next $5,000, and half a percent above $10,000, all of it lost when the return or the payment is late.

At year end, the W-2 copies go to the Department with Form MO W-3, due the last day of January when filed electronically and the last day of February on paper.

The two city earnings taxes

Missouri has no county income taxes and no township levies. It has exactly two cities with local income tax, and if your business sits outside both and none of your employees live or work in either one, this section does not apply to you at all.

The St. Louis payroll expense tax is the piece that is easiest to miss, because it behaves differently from everything around it. It is not a withholding but an employer cost on gross compensation paid for work in the city.

The Collector of Revenue takes the payroll expense tax quarterly, alongside the earnings tax, on Forms W-10 and P-10. A business that correctly withholds the 1 percent and never files the P-10 has satisfied only half the obligation.

Both city taxes go back to voters every five years under RSMo 92.115, and if a vote failed, state law would start reducing the tax. Non-residents who work only partly inside city limits owe the tax only on the wages earned for that work, so days worked elsewhere fall outside it.

The pay frequency rule that catches new employers

In Missouri, corporations must pay most employees at least twice a month, and that rule covers a large share of businesses. Most states set a minimum pay frequency in law, as the Department of Labor state payday table shows, but this is the Missouri requirement most likely to be discovered after the fact.

The consequence for software selection is direct. A monthly payroll cycle is not available to most Missouri corporations under RSMo 290.080, so any provider that charges per payroll run rather than a flat monthly fee costs at least twice what a monthly-cycle comparison would suggest.

Nearly all the providers below include unlimited runs, but confirm it rather than assume it, particularly with quote-based vendors, where run-based pricing occasionally appears.

10 payroll providers for Missouri employers compared

Every provider below files Missouri state withholding and unemployment. The question that separates them in practice is whether the Kansas City or St. Louis earnings tax is handled, which is not universal.

OnPay

OnPay sells one payroll plan at $49 per month plus $6 per employee, so there is no tier to climb; HR tools and time tracking are paid add-ons. Year-end W-2 and 1099 filing is included, and the first month is free.

Tax filing covers federal, state, and local taxes in all 50 states with no multi-state surcharge, which matters in a state bordered by eight others and holding reciprocity with none of them.

Gusto

Gusto is a common first payroll purchase for US small businesses. Tax filing runs automatically across federal, state, and local jurisdictions, year-end processing carries no extra charge, and the Simple plan runs $49 per month plus $6 per employee after a base increase from $40 during 2025.

The Missouri catch is that Simple covers single-state payroll only. Given that the Kansas City metro straddles the Kansas line and the St. Louis metro reaches into Illinois, one cross-border hire moves the account to Plus at $80 plus $12 per employee.

Patriot Software

Patriot Full Service is the lowest-cost full-service payroll on this page at every headcount modeled below, at $37 per month plus $5 per employee. It covers federal, state, and local tax filing, though new hire reports stay with the employer. Basic at $17 plus $4 only calculates payroll and leaves depositing and filing to the employer.

Unlimited payroll runs matter more than usual here given the twice-monthly requirement. Additional state filings cost $12 per month each. For a single-state Missouri business, nothing else on this page costs less.

QuickBooks Workforce Payroll

Workforce Payroll, formerly QuickBooks Payroll Core and renamed in May 2026, runs $50 per month plus $7 per employee after the per-employee increase of July 1, 2026. The reason to pick QuickBooks is unchanged: if the books already live in QuickBooks Online, payroll entries land in the general ledger with no export step.

Federal and state tax filing is included on every tier, but certain local taxes are available only on Workforce Premium and Elite, so check the Kansas City and St. Louis earnings taxes before choosing the entry tier.

SurePayroll

SurePayroll is owned by Paychex and aimed at very small and household employers, at $29 per month plus $7 per employee. The distinguishing feature is a flat $9.99 monthly multi-state fee regardless of how many states are involved, which beats per-state pricing for anyone operating across two or three of Missouri's many borders.

Local taxes cost extra: SurePayroll adds a separate fee in areas that require them, so in Missouri a Kansas City or St. Louis payroll costs more than the headline rate.

Square Payroll

Square Payroll is full-service payroll at $35 per month plus $6 per person paid, with tax filing included. For a Missouri restaurant or retail business already running Square point of sale, timecards import from the register and card tips import for W-2 employees.

The import matters in Missouri because the tipped minimum requires the employer to top up to $15.00 whenever tips fall short, which needs accurate hour and tip data every pay period.

Paylocity

Paylocity is a full HR and payroll platform aimed above the smallest end of the market: its clients average more than 150 employees, per its annual report. It prepares and files state and local withholding returns, and pricing is quote-only.

For a Missouri company moving into the mid-size range or operating on both sides of a metro state line, Paylocity becomes a reasonable candidate.

ADP RUN

ADP describes the same tax compliance operation behind every RUN package: it calculates, files, deposits, and reconciles payroll taxes, responds to agency inquiries, and pays the resulting fines if it makes a filing error.

Multi-jurisdiction payroll, meaning more than one state or local jurisdiction in a pay period, is included in all four packages. That is the part that matters in Missouri, for the city earnings taxes and the cross-border hires the metros generate. ADP publishes no rates, so every package from Essential to HR Pro is quoted individually, and no contract is required.

Paychex Flex

Paychex Flex is a service relationship rather than a software subscription, with a payroll specialist included on the Complete package. Pricing is quote-only across the Basic, Foundations, Advanced, and Complete packages, and the standard service agreement can be ended on 30 days' notice.

The Missouri argument for Paychex is concrete: when a St. Louis payroll expense tax notice arrives for a filing nobody knew existed, having someone to call has real value.

Rippling

Rippling puts payroll, HR, and IT provisioning on one unified employee record and data model. Its small-business page starts payroll plans at $8 per user per month plus a $40 monthly base fee, while its pricing page is a quote form. Its blog starts the core platform at $8 per employee and prices the payroll module at $8 billed annually or $10 billed monthly, so configured quotes run higher than that start.

Rippling runs multi-state tax registration inside the same workflow, which is genuinely useful in the border metros, but the platform is overbuilt for a small single-location Missouri business.

What each provider actually costs a Missouri employer

The table below models published rates at three headcounts plus the second-state column, which carries unusual weight here because Missouri borders eight states and has reciprocity with none of them.

Two patterns hold. First, Patriot and Square undercut OnPay, Gusto Simple, and QuickBooks at every headcount, and Patriot is the cheapest published option at all three. SurePayroll starts cheap, but its higher per-employee fee carries it past OnPay and Gusto Simple at the largest headcount.

The other pattern is the second-state column, which matters more in Missouri than in most states because both major metros cross a border: Kansas City reaches into Kansas and St. Louis into Illinois. Gusto Simple is competitive until one such hire forces the Plus tier, at which point a 15-person payroll jumps from $139 to $260.

Choosing a payroll provider for Missouri

Four questions separate providers that will work here from providers that will generate notices.

Beyond the payroll engine, the requirement most commonly missed is the 20-day new hire report. Most full-service plans file it automatically and Basic tiers generally do not, which leaves a deadline running on every hire.

Payroll services for a Kansas City employer

A payroll service working in Kansas City has to do one thing a plain Missouri setup does not: withhold the 1 percent earnings tax and file it with the city rather than the state. The Revenue Division collects it on Form RD-110, a quarterly return, with monthly or quarter-monthly payments on the same schedule the state assigns for withholding.

Two more requirements sit behind it. Form RD-113 reconciles the year by January 31 and carries the W-2 detail with it, and both returns have to be filed electronically. A quarter with nothing withheld still needs an RD-110. Providers that already file for Kansas City employers send those returns through the city bulk filing program, so ask about it by name.

The other Kansas City question is which side of the state line your people sit on. The metro runs into Kansas, Missouri grants no reciprocity, and the earnings tax follows where the work is performed rather than where your office is.

Three kinds of Kansas City payroll services can handle that: a national platform, a local accounting firm, and a professional employer organization. What separates them is whether the city filings come with the service or come back to you.

Before you choose

FirstHR is an onboarding and HR platform, not a payroll provider. Running payroll, the duty to file payroll taxes, and benefits administration belong to the providers above, and if payroll is the problem you are solving, one of them is your answer.

What we handle is the layer underneath, and Missouri puts two specific demands on it. Correct withholding depends on a Form MO W-4 that was actually collected, since the filing status on it drives the entire calculation and an employee without one is withheld as single.

Same-day final pay on termination is the second demand: the offboarding conversation and the payroll run have to happen together rather than a week apart.

FirstHR covers onboarding workflows that put Form MO W-4 on the first-day task list for each new hire, e-signatures on offer letters and policy acknowledgments, and employee records that keep the completed form on file, for US small businesses at a flat $98 a month for up to 10 people or $198 for 11 to 50. The form itself is filled in outside the platform.

If the recurring failure is paperwork arriving late or incomplete rather than the tax math, that is a different problem than payroll processing, and it is the one we built for.

Frequently Asked Questions

What payroll taxes do Missouri employers withhold?

State income tax on eight brackets topping out at 4.7 percent, calculated after a standard deduction set by filing status on Form MO W-4, plus a 1 percent city earnings tax for anyone working in Kansas City or St. Louis. Residents of either city owe that earnings tax wherever they work.

Employers separately pay unemployment on the first $9,000 of wages, and St. Louis employers pay a 0.5 percent payroll expense tax.

Does Missouri have a state W-4 form?

Yes. Every employee completes Form MO W-4 for Missouri withholding on top of the federal W-4, and anyone who never turns one in is withheld as single. The form no longer uses numerical allowances: filing status drives the standard deduction, which for 2026 is $16,100, $32,200, or $24,150 depending on status. Employees can still ask for additional or reduced withholding.

What is the Missouri unemployment wage base?

$9,000 per employee for 2026, down from $9,500, with statute setting a floor of $7,000 and a ceiling of $13,000. New employers pay 2.376 percent and qualifying nonprofits 1 percent, while experienced employers fall between zero and 6 percent before any surcharge.

Who pays the Kansas City and St. Louis earnings tax?

Both cities charge 1 percent to residents wherever they work and to non-residents on income earned in the city, and employers withhold and remit it for work inside city limits. St. Louis adds a separate 0.5 percent payroll expense tax paid by the employer, filed on Form P-10 with the W-10. These are the only local income taxes in Missouri.

How often must Missouri employers pay employees?

Corporations must pay at least twice per month within 16 days of the pay period close. Executive, administrative, professional, and commission sales employees may be paid monthly. A terminated employee is owed final wages on the day of discharge.

What is the Missouri minimum wage?

$15.00 per hour since January 1, 2026. House Bill 567 kept the rate set by Proposition A while removing the Consumer Price Index adjustment scheduled for 2027 and repealing the statewide paid sick leave mandate. The tipped minimum is $7.50 with employer top-up to the full rate.

Does Missouri have reciprocal tax agreements with other states?

No, with none of its eight neighbors, as the Department of Revenue employer tax guide states. An employee living in Kansas or Illinois and working in Missouri has Missouri tax withheld on Missouri-source wages, and resolves any double taxation through a credit on their home state return rather than through payroll.

How much does payroll software cost for a Missouri small business?

At 5 employees, published October 2026 rates run roughly $62 for Patriot Full Service, $64 for SurePayroll, $65 for Square Payroll, $79 for OnPay or Gusto Simple, and $85 for QuickBooks Workforce Payroll. At 50 employees the same plans land between $287 and $400. ADP RUN, Paychex Flex, and Paylocity quote individually.