A complete guide to filing quarterly taxes for an LLC

Filing quarterly taxes for an LLC can penalize you even when your annual return shows a refund. The IRS charges underpayment penalties on each estimated tax installment, so an overpayment in September still leaves an April shortfall on the books. Treating those due dates like calendar quarters is a common reason LLC owners fall behind on their federal tax obligations without realizing it.

Filing quarterly taxes for an LLC means paying the IRS in four Form 1040-ES installments (April 15, June 15, September 15, and January 15). Each installment covers both federal income tax and 15.3% self-employment tax on your share of pass-through business profit. Below, you'll see who owes estimated payments, how your LLC's tax classification changes the form, how to calculate each installment, and the safe harbor rules that prevent underpayment penalties.

Does your LLC have to file quarterly taxes?

Your annual tax projection shows whether quarterly estimated payments apply. If it shows a federal tax balance remaining after withholding and credits, the IRS may expect installments during the year to cover that gap.

With a default-taxed LLC (one that hasn't elected corporate tax treatment), profit passes through to your individual return without automatic withholding. You pay the tax personally on your Form 1040, which is why quarterly estimated payments exist. They're your way of prepaying the IRS on self-employment income you've already earned, and you reconcile them against your final tax bill on your annual return.

The $1,000 rule that triggers quarterly payments

You generally need to file quarterly taxes if you expect to owe $1,000 or more in federal tax for the year after withholding and credits. Your projection includes both income tax and self-employment tax on your share of profit. Include both parts in your projection, self-employment tax alone can push a small business with modest profit past the threshold. If you're new to the SE portion, see our self-employment tax basics for a fuller breakdown.

When W-2 withholding covers your LLC tax bill

Withholding from a W-2 job counts toward your annual tax bill, and your spouse's paycheck withholding also counts if you file jointly. The IRS generally treats paycheck withholding as paid evenly throughout the year, even if your employer withheld more of it later. That means you may be able to increase W-2 withholding instead of sending separate estimated tax payments.

Enough withholding from a day job may cover the tax on a modest LLC profit. If the $1,000 threshold doesn't apply, you can skip estimated payments and settle the bill when you file.

Which IRS forms your LLC needs for estimated taxes

Your LLC's tax classification determines who makes estimated payments and which form or worksheet applies. Use this matrix first, then read the matching subsection for annual-return details. Most LLC owners use Form 1040-ES. If your LLC elected C-corporation treatment, however, the company pays its own estimated taxes.

Multi-member LLC (Form 1065 and K-1s)

A multi-member LLC files Form 1065 to report business results, then passes profit through to members via Schedule K-1. Each member bases their Form 1040-ES payments on the share reported on their K-1.

You owe tax on your share even if the LLC didn't distribute the cash to you, a rule that can catch owners off guard when they leave profit in the business.

LLC taxed as an S-corp

S-corp owners pay themselves a salary through payroll, and the tax withheld from that salary counts toward their annual bill. You may still need estimated payments if withholding won't cover the full amount, often because shareholder distributions on top of salary increase your taxable income. Many owners cover the difference by increasing salary withholding instead of sending separate payments. 

LLC taxed as a C-corp

An LLC taxed as a C corporation pays its own tax on Form 1120 and makes estimated payments at the entity level. The IRS discontinued Form 1120-W. If your LLC chose C-corp taxation, calculate its payments with the estimated tax worksheet in the Form 1120 instructions and keep the completed worksheet in your records; the IRS doesn't require you to file it.

How to calculate each quarterly tax payment

Calculate each quarterly payment by moving through a connected sequence: project annual profit, calculate self-employment tax, calculate federal income tax, and allocate the total across the required payment periods. Start with a current profit-and-loss statement. The steps below follow the Form 1040-ES worksheet.

Step 1: Project net profit for the year

Estimate your full-year revenue, then subtract deductible business expenses. Last year's return gives you a useful baseline. Update it for contracts you've signed, rate increases you've made, and costs you already know are coming.

Step 2: Calculate self-employment tax

Multiply your projected net profit by 92.35% to get the amount subject to self-employment tax. Then multiply that result by 15.3%, the combined Social Security and Medicare rate for self-employed workers, per the IRS. Check the current IRS SE tax page for the annual Social Security wage base and any additional Medicare tax that applies to higher earners. Half of this SE tax is deductible on your income tax calculation, so carry that deduction into Step 3.

Step 3: Calculate federal income tax

Work through these subtractions in order:

1. Start with projected net profit.

2. Subtract the deductible half of self-employment tax.

3. Subtract the standard deduction for your filing status.

4. Subtract the Qualified Business Income (QBI) deduction if you qualify.

5. Apply the current-year federal tax brackets to the remaining taxable income.

The result is your projected federal income tax for the year, which you'll add to the SE tax from Step 2 to get your total expected tax. You'll find the applicable standard deduction, brackets, and QBI thresholds in the IRS annual inflation adjustments revenue procedure released each fall.

Worked example (2024 illustrative figures — always confirm with the current-year Rev. Proc.): Say you and your spouse expect $80,000 in profit from your LLC this year, with no other income.

SE tax ≈ $80,000 × 0.9235 × 15.3% = $11,304.

Half of that ($5,652) is deductible.

Taxable income = $80,000 − $5,652 − $29,200 (2024 MFJ standard deduction, per IRS Rev. Proc. 2023-34) = $45,148, and QBI can reduce this further.

Federal income tax at 2024 MFJ brackets ≈ $4,800. Total expected tax ≈ $16,104, or roughly $4,026 per quarterly installment.

Step 4: Divide across the payment periods

Divide your expected tax by four if your income is steady. If your income swings sharply by season, use the IRS annualized income installment method. You calculate each payment from what you earned in that period and report the calculation on Form 2210 Schedule AI. IRS Publication 505 has the full worksheet.

How and when to pay quarterly taxes

You can pay federal estimated taxes online through IRS Direct Pay, EFTPS, the IRS2Go app, credit or debit card, or by mailed check on four annual deadlines: April 15, June 15, September 15, and January 15. Schedule each payment before its deadline and report every installment on your annual return.

The four federal estimated tax deadlines

Payment periods run on an uneven schedule. For most tax years, the deadlines are:

If a deadline falls on a weekend or federal holiday, the IRS moves it to the next business day.

Paying quarterly taxes online

The IRS accepts estimated payments through several online channels, each with different setup requirements and record-keeping strengths:

• IRS Direct Pay: free ACH transfer from your bank account; no enrollment needed.

• EFTPS: the Treasury's Electronic Federal Tax Payment System; requires advance enrollment and keeps a full payment history for filing.

• IRS2Go app: mobile payment from your phone.

• Credit or debit card: via the two IRS-authorized processors (Pay1040 and ACI Payments); processor fees apply.

Whichever channel you use, save the confirmation number so you can match each payment to the correct installment on your annual return.

Paying by mail

Follow the Form 1040-ES instructions. Make the check payable to "United States Treasury" and write your Social Security number and the applicable Form 1040-ES tax year on the memo line. Mail the payment early enough to get a postmark by the due date.

Keep the 1040-ES worksheet, the date and amount of each payment, and confirmation numbers from Direct Pay or EFTPS (or proof of the postmarked check).

Your quarterly tax set-aside worksheet

Beyond the quarterly payment itself, calculate a set-aside percentage you can move out of every client deposit as it lands. Complete these items annually to calculate both amounts:

• Projected net profit for the year: $____

• Estimated self-employment tax from the current Form 1040-ES worksheet: $____

• Income tax after deductions: $____

• Total expected tax: $____

• Amount to set aside for each required payment: $____

• Set-aside rate on each deposit: ____%

Use the final percentage to move the right share into a dedicated tax savings account every time revenue arrives, before payroll and supplies can eat into it. Relay's percentage-based transfer rules — available on every plan, including the no-monthly-fee Starter tier — move your chosen share into a dedicated tax checking account automatically as each deposit lands, so the set-aside runs on its own.

State quarterly taxes and franchise fees

Paying the IRS covers your federal bill only; each state runs its own estimated tax and LLC-fee schedule. Here's how a few high-LLC states handle it:

Ask your state's revenue department whether you owe estimated taxes on your share of business profit and whether the LLC owes any company-level tax or annual fee. For owners juggling both federal and state estimates, Relay lets you open up to 20 checking accounts, so you can keep a federal tax account and a state tax account funded at their own transfer rates and both walled off from operating cash.

For a broader look at multi-state obligations, see our overview of state tax obligations.

Avoiding underpayment penalties

Pay enough by each IRS deadline to avoid an underpayment charge on that installment. The safe harbor rules give you clear payment targets that prevent the penalty.

The safe harbor rule

Hit either target and you're protected. Per the IRS estimated tax rules, your combined withholding and estimated payments must equal at least:

• 90% of this year's total tax, OR

• 100% of last year's total tax (110% if your prior-year adjusted gross income exceeded $150,000, or $75,000 if married filing separately).

Meeting either target for the year protects you from the underpayment penalty even if your final tax bill comes in higher than expected. Using last year's tax makes planning easier because it's a fixed number you can pull from your prior return early in the year and divide across payments. If your LLC is new and you don't have a prior-year return, use the current-year 90% method.

The underpayment penalty rate

Under IRC §6621, the underpayment rate for non-corporate taxpayers equals the federal short-term rate plus 3 percentage points. Interest compounds daily under IRC §6622. The rate applies for the period each installment remains unpaid. Because the rate resets quarterly, check the current IRS notice for the applicable rate before you calculate any charge.

Missed quarterly tax deadlines

Pay as soon as you notice, because sooner limits the charge. If you can't pay the full annual balance when your return is due, file your return anyway. The IRS imposes separate failure-to-file and failure-to-pay penalties, and delaying the return can multiply the total cost.

Mid-year adjustments to quarterly payments

Rerun the 1040-ES worksheet whenever your income changes enough to affect your estimate, and raise or lower the remaining payments accordingly. If a casualty or disaster caused an underpayment, file Form 2210 with supporting records to ask the IRS to waive the penalty for reasonable cause.

Set up your tax account before the next deadline

Filing quarterly taxes becomes manageable when you calculate the target, treat each payment as money already committed, and separate the tax share as revenue arrives. Review your estimate whenever income changes so your transfer rate and remaining payments stay aligned with the latest projection.

When tax money stays in your operating account, every ordinary expense can compete with the next IRS payment. Opening a Relay account gives you a dedicated tax checking account beside your operating account and percentage-based transfer rules that move your chosen share from each deposit, keeping quarterly tax money separate and visible.

Frequently asked questions

Do I still have to file quarterly taxes if my LLC lost money or had no income?

If you project a net loss or below-threshold profit for the year, you generally don't owe estimated payments. Still file your annual return to document the loss, which can offset future income or a spouse's W-2 wages on a joint return.

Can I pay LLC quarterly taxes with a credit or debit card?

Yes. Per the IRS card payment page, the IRS accepts card payments through two authorized processors: Pay1040 and ACI Payments. Each charges a percentage-based fee for credit cards and a flat fee for debit, and consumer card rates and commercial or Amex rates differ. Check the IRS page for current amounts. This route generally makes sense only if rewards or cash-flow timing outweigh the fee.

What percentage of my income should I set aside for quarterly taxes?

Set aside 25%–30% of net profit if you're an LLC owner without a W-2 job. That range covers federal income tax plus the 15.3% self-employment tax for most owners. Owners in higher federal brackets or high-tax states typically need to save more. Use the set-aside worksheet in this guide to calculate your specific rate based on your projected profit.

Do I need an EIN to pay quarterly taxes for my LLC?

Single-member LLCs taxed as disregarded entities pay estimated taxes under the owner's Social Security number using Form 1040-ES, so no EIN is required. You'd only need an EIN if the LLC has employees, elected corporate taxation, or has multiple members.

Are quarterly estimated tax payments deductible as a business expense?

Estimated payments cover federal income tax and the income-tax portion of self-employment tax, both of which are personal liabilities, so they never appear on Schedule C. Your Form 1040 does allow an above-the-line adjustment for half of your self-employment tax, and that deduction is already built into the 1040-ES worksheet.