Missouri payroll tax and registration guide

Why is this important?

To maintain compliance with state payroll tax regulations, you must provide the following information before you can use OnPay to run payroll:

State Employer Identification Number and state/local tax IDs
Tax rates - State tax offices set these rates based on the type, age, and size of your business
TPA and power of attorney - Most tax offices require this before we can submit quarterly wage reports and deposits on your behalf

This information must be provided and maintained by you in order for OnPay to accurately file and deposit tax payments for your company. OnPay is not responsible for any penalties or interest that incur due to missing or incorrect company tax information.

Each state has its own requirements, so if you pay employees in more than one state, you’ll find separate tax guides for each state.

Let Middesk handle your state tax registrations

Want help registering your business with state agencies? We've partnered with Middesk to make it simple for you to stay compliant in your state — and every state — when hiring employees.

Register with state agencies and get the tax IDs you need within minutes
Manage all your government accounts in one place using Middesk's intuitive platform
Stay compliant by managing agency mail and notices from your Middesk dashboard
Foreign Qualify with the Secretary of State to create payroll tax accounts

Learn more about Middesk

See what information you need to provide OnPay, and what taxes and filings OnPay handles for Missouri Employers.

Information OnPay needs from you

Use this checklist to make sure you’ve covered everything required to set up your account as a Missouri employer, so OnPay can accurately file and pay taxes on your behalf:

All Missouri employers	What is this?
Make sure your business is registered with the Missouri Department Revenue	Allows your business to file and pay taxes in Missouri More info >
Make sure your business is registered with the Missouri Department of Labor	Allows your business to pay required unemployment insurance in Missouri More info >
Provide OnPay with your Missouri Withholding Tax Account Number and deposit schedule	The employer identification number issued by the Missouri Department of Revenue More info >
Provide OnPay with your Missouri Unemployment Account Number	A 6-digit number unique to your account with the Missouri Department of Labor More info >
Provide OnPay with your Missouri Unemployment (SUI) Rate	A tax rate you receive annually from the Missouri Department of Labor More info >

Taxes and filings OnPay handles for Missouri Employers

Withholding Tax

Form MO-941 (Filing)	Employer's Withholding Tax	- Monthly, Quarterly, Annual
Form MO W-3 (Filing)	Transmittal of Tax Statements	- Annual
State W-2 (Filing)	Wage and Tax Statement	- Annual

Unemployment Insurance Tax

MODES-4 (Filing)

Employer's Quarterly Contribution and Wage Report

- Quarterly

Other

New Hire Report

Missouri Report of New Hires

- As required

Where you can find the tax account numbers you need

If you are an existing employer who has previously run payroll in the state of Missouri, you likely already have the IDs and online accounts needed for OnPay to process your tax filings.

If you are a new employer in Missouri, you will need to register your business with the Department of Revenue and Missouri Department of Labor. This must be completed for OnPay to be able to file and pay your Missouri taxes.

Withholding Tax Account Number

Existing Missouri Employer:

You can find your Withholding Tax Account Number on notices received from the Missouri Department of Revenue. If you cannot locate this document or account number, please call the Missouri Department of Revenue at (573)-751-3505 to request it.

New Missouri Employer: Register with the Missouri Department Revenue

Visit the Missouri Department of Revenue where you can use their online registration system
- You'll be able to register with both the Missouri Department of Revenue and Department of Labor
- You can also download the Missouri Tax Registration Application (Form 2643)
- Before registering, make sure you have all required information listed under “Checklist for Completing Application” on Form 2643
After you have completed your online registration, you'll receive a confirmation number and additional information about your registration (Allow 2-3 business days for processing)
- Please maintain the confirmation number for your records
- If you have any questions, contact the Missouri Department of Revenue at (573)-751-3505

Unemployment Account Number and Tax Rate

Updated January 1, 2025