How to Pay Missouri Income Tax and What Happens If You Don't
Where Missouri Income Tax Goes and How to Send It
Missouri collects income tax through the Department of Revenue, and you send your payment directly to them—not to your employer or a local office. If you work in Missouri, your employer withholds tax from each paycheck and sends it to the state on your behalf. If you're self-employed, own a business, or have income your employer doesn't withhold from, you pay the state directly, usually four times a year in estimated payments or all at once when you file your annual return.
The state accepts payments online through its official portal, by mail, by phone, or through an authorized payment processor. The method you choose affects when the state receives your money and whether you face a late penalty. Online and phone payments typically post within one business day. Mailed checks take longer—the state's processing center is in Jefferson City, and mail delivery adds several days to the timeline.
Key Takeaways
- Missouri income tax is sent to the Department of Revenue, either through employer withholding or by you paying directly if you're self-employed or have other income sources.
- You can pay online at the Missouri Department of Revenue website, by mail, by phone, or through an authorized payment processor, and online payments post fastest.
- If you owe tax when you file your return, you can pay it immediately with your return or set up a payment plan if you cannot pay in full.
- Late payments trigger a penalty of 0.5% of the unpaid tax per month, plus interest that compounds daily, and the state can place a lien on your property or garnish your wages.
- If you cannot pay what you owe, contact the Department of Revenue to discuss a payment plan or hardship relief before the due date.
Paying Tax Withheld by Your Employer
If you receive a W-2 at the end of the year, your employer has already withheld Missouri income tax from your paychecks and sent it to the state. You do not send this money yourself. When you file your state return, the Department of Revenue compares what was withheld to what you actually owe. If too much was withheld, you receive a refund. If too little was withheld, you owe the difference.
The amount withheld depends on the W-4 form you filled out when you started your job. If you want to change how much is withheld—for example, to reduce your refund or to avoid owing money at tax time—you can submit a new W-4 to your employer at any time. The change takes effect on your next paycheck.
Paying Self-Employment Tax and Estimated Quarterly Payments
If you are self-employed, own a business, or have income from sources that do not withhold tax (such as rental income, freelance work, or investment gains), you are responsible for sending money to Missouri throughout the year. The state calls these estimated tax payments, and they are due four times annually: April 15, June 15, September 15, and January 15 of the following year.
You calculate your estimated payment by predicting your total income for the year, subtracting deductions, and dividing by four. If your income changes during the year, you can adjust future payments. If you underpay, you owe interest on the shortfall when you file your return. If you overpay, the state refunds the difference or credits it to next year's estimated payments.
To make an estimated payment, log into the Missouri Department of Revenue's online payment system, call their payment line, or mail a check with a voucher form (available on the department's website). Online and phone payments are processed the same day; mailed payments take longer and may be considered late if they arrive after the due date.
Paying Tax Owed When You File Your Return
When you file your Missouri state income tax return, you may owe additional tax beyond what was withheld or what you paid in estimated payments. You can pay this balance immediately using the same methods available year-round: online, by phone, by mail, or through an authorized processor. If you file electronically, you can authorize an electronic withdrawal from your bank account on the date you choose.
If you cannot pay the full amount by the due date, you have options. You can request a payment plan from the Department of Revenue, which allows you to pay in installments over several months. The state charges a setup fee (currently $25 for online plans) and interest on the unpaid balance. You can request a plan online, by phone, or by mail before or after the due date, though requesting before the due date may reduce penalties.
If you face genuine hardship—job loss, medical emergency, or other circumstances beyond your control—you can request hardship relief or a temporary delay in collection. Contact the Department of Revenue's taxpayer assistance line to discuss your situation. The state does not forgive the debt, but it may pause collection efforts or reduce penalties while you stabilize your finances.
What Happens If You Miss the Deadline
Missouri charges a late payment penalty of 0.5% of the unpaid tax for each month (or part of a month) that the payment is late. This penalty compounds, so the longer you wait, the more you owe. In addition, the state charges interest on the unpaid balance, calculated daily at a rate set quarterly. Interest also compounds, meaning you pay interest on top of interest.
If your payment is more than 90 days late, the state may file a tax lien against your property. A lien is a legal claim that gives the state a right to your assets if you sell property or receive a large sum of money. A lien damages your credit and can prevent you from refinancing a mortgage or taking out loans. The state can also garnish your wages, meaning it orders your employer to send a portion of your paycheck directly to the Department of Revenue until the debt is paid.
The sooner you pay, even if you cannot pay in full, the lower your total cost. A partial payment stops the clock on some penalties and reduces the interest that accrues. If you are unable to pay by the due date, contact the Department of Revenue before the deadline to set up a plan or discuss hardship options.
Payment Methods and Processing Times
| Payment Method | Processing Time | When to Use It |
|---|---|---|
| Online (Missouri Department of Revenue website) | Same day or next business day | Fastest option; requires bank account or debit card |
| Phone (authorized payment processor) | Same day or next business day | Quick if you do not want to use a website |
| Mail (check or money order) | 5 to 10 business days after arrival | Only if you cannot pay online or by phone; mail early to avoid late penalties |
| Authorized payment processor (third-party vendor) | Same day or next business day | Alternative to state website; may charge a convenience fee |
If you mail a check, the postmark date is what matters for determining whether you are late—not the date the state receives it. However, the state does not process the payment until it arrives, so mail your check at least one week before the due date to be safe. If you are cutting it close, use online or phone payment instead.
Frequently Asked Questions
Can I pay Missouri income tax by credit card?
The Missouri Department of Revenue does not accept credit cards directly, but authorized third-party payment processors do. These processors charge a convenience fee (typically 2% to 3% of the payment) in addition to your tax. You can find the list of authorized processors on the state's website. For most people, paying by debit card or bank transfer online avoids this extra cost.
What if I filed my return late and now owe tax?
You owe both the tax and a failure-to-file penalty, which is separate from the late payment penalty. The failure-to-file penalty is 5% of the unpaid tax per month, up to 25% total. Pay as soon as possible to stop both penalties from growing. If you have a legitimate reason for filing late (such as a death in the family or a serious illness), you can request that the Department of Revenue waive or reduce the penalty.
Can I set up a payment plan if I owe a small amount?
Yes, but the setup fee ($25 for online plans) may cost more than the tax itself if you owe very little. If you owe less than $100, it may be cheaper to pay in full immediately. For larger amounts, a payment plan can spread the cost over time, though you will pay interest on the unpaid balance each month.
What if my employer withheld too much tax and I am owed a refund?
When you file your return, the Department of Revenue calculates the refund and sends it to you automatically. You do not need to do anything except file. Refunds are typically issued within 30 to 60 days of filing, though the state can take longer during peak season. You can check the status of your refund on the Department of Revenue's website.
Does Missouri allow payment plans for estimated tax payments I missed?
If you missed an estimated payment deadline, you can pay it at any time, and the state will charge interest and penalties based on how late it is. You can pay the missed amount in full or request a payment plan. Contact the Department of Revenue to discuss your options before penalties grow larger.