Start with a federal Employer Identification Number if you don’t have one already. You need this before you can register with Missouri or process any payroll. Apply directly through the IRS website and you’ll get it immediately.

Register with the Missouri Department of Revenue for withholding tax. You’ll need your EIN and business information. Missouri requires employers to withhold state income tax from employee wages. The registration gives you an account number for filing and paying withholding taxes.

Set up withholding correctly. Federal withholding uses W-4 forms from employees. Missouri withholding uses the employee’s W-4 or Missouri W-4 if they file one. You’ll withhold based on their filing status and number of allowances claimed. Get this wrong and employees owe money at tax time or you owe back taxes and penalties.

Register for local earnings taxes if you have employees working in Kansas City or St. Louis. Both cities impose 1% earnings taxes on wages earned within city limits. You withhold this separately from state and federal taxes and remit it to the respective city. Miss this and you’re non-compliant with local requirements.

Choose how you’ll run payroll. Manual calculation works for one or two employees if you’re confident with the math and filing requirements. Payroll software like QuickBooks or Gusto automates calculations, tax deposits, and quarterly filings. Full payroll services handle everything so you just approve hours and employees get paid.

File quarterly reports with Missouri and the IRS. Form 941 goes to the IRS quarterly reporting wages and taxes withheld. Missouri requires quarterly wage and tax reports. Miss filing deadlines and penalties start accumulating immediately.

Make tax deposits on schedule. Federal payroll taxes usually deposit semi-weekly or monthly depending on your total tax liability. Missouri withholding deposits follow a similar schedule. The deposits must happen before you file the quarterly reports or you’re late and facing penalties.

Workers’ comp insurance is required in Missouri for most employers. You need coverage before you hire your first employee. Rates vary by industry and your claims history. This isn’t optional and the state enforces it.

The setup itself isn’t complicated but getting it wrong creates problems that compound. Incorrect withholding means employees get surprise tax bills. Late deposits mean penalties. Missing local taxes in Kansas City or St. Louis means you’re non-compliant and will eventually get caught.

Most small businesses either use payroll setup services to configure everything correctly from the start or outsource the entire payroll function. The cost of getting it wrong usually exceeds what professional help costs, especially when you factor in the time you spend researching requirements and hoping you did it right.