Let’s see if this sounds familiar. It's the day before a quarterly tax deadline, and that familiar panic sets in: Did you calculate taxes right? How’s your cash flow? When you're juggling payroll, invoicing, and actual revenue-generating work, figuring out how to pay quarterly taxes online shouldn't add to tax day stress.
You can pay your quarterly taxes online using three reliable options: IRS Direct Pay (if you want a free option that takes 5 minutes), EFTPS (if you prefer an automated option that requires one-time setup), and debit or credit card (if you love convenience and don’t mind fees).
In this guide, we’ll share a guide to quarterly taxes, including how to calculate payments without tying up cash you need for growth, which online method fits your workflow, and how to automate the entire process so you never face tax season panic again.
What taxes do self-employed people pay?
Running your own business means you're covering both sides of the tax equation. The self-employment tax hits you for 15.3% of net profit (12.4% for Social Security plus 2.9% for Medicare). Then regular income tax applies based on your bracket, just like everyone else.
The quarterly tax payments for business owners exist to replace the automatic withholding that happens with W-2 paychecks. So every three months, you send the IRS a slice of both taxes. The math, the cash reserves, the deadline tracking—all of it lands on you.
Most states also impose their own income or gross receipts taxes, which often follow separate calendars that align with federal deadlines.
Who needs to file and pay estimated quarterly taxes?
If you expect to owe at least $1,000 in federal taxes when you file your return, you're required to make quarterly payments. This includes freelancers, consultants, independent contractors, sole proprietors, single-member LLCs, partnerships, and gig-economy workers. Even side income counts: substantial 1099 earnings trigger quarterly requirements regardless of your W-2 job.
You're only exempt if employer withholding covers your total tax bill or you'll owe under $1,000 for the year. And if you file late or underpay, you risk incurring penalties from the IRS.
How to estimate your quarterly tax payments as a business owner
You can calculate quarterly payments using Form 1040-ES (the IRS worksheet for projecting profit and deductions) or use a faster percentage-based method that most business owners prefer. Both get you to the same place: accurate payments that avoid penalties.
Here’s how the percentage method for estimating quarterly tax payments works in four steps:
Set your baseline percentage: Transfer 25 to 30% of every business deposit into a separate tax account. This covers both self-employment tax and income tax for most businesses.
Fine-tune your percentage using the IRS Tax Withholding Estimator: Don't forget that most pass-through owners qualify for the 20% Qualified Business Income deduction (more on this in the next section).
Use safe-harbor rules for protection: Pay 100% of last year's total tax (110% if you earned over $150K) or 90% of this year's bill. Either approach keeps penalties away (and the IRS happy) even if your income jumps mid-year.
Adjust quarterly based on your actual income: Review your profit each quarter and recalculate if revenue changes significantly. For example, you’ll need to increase your tax allocation immediately if you’re a home services contractor landing three major projects in Q2.
This quarterly check-in prevents two tax problems: overpaying, which ties up cash you need for business expenses like equipment or hiring, and underpaying, which triggers penalty fees that compound every quarter.
When we’re talking about estimates, there’s one more item most businesses need to consider: QBI deduction.
What is a Qualified Business Income (QBI) deduction?
Qualified Business Income is the net profit from your business. Essentially, it’s what's left after you subtract expenses from revenue. The QBI deduction (also called Section 199A) lets you deduct up to 20% of that income on your personal tax return, which directly reduces your taxable income and lowers your quarterly tax payments.
Most sole proprietors, partnerships, S-corporations, and LLCs qualify for the full deduction if their taxable income stays under $191,950 (single) or $383,900 (married filing jointly). High earners and professionals in specified service fields (like law, medicine, and consulting) face additional wage and property limits that can phase out the deduction.
When you're calculating quarterly payments, the QBI deduction lowers the income figure you're working from. Form 1040-ES has a dedicated line for it, so you can include it when estimating your payments.
If you're using the percentage method, this deduction is already baked into the 25-30% baseline. And if your income approaches those thresholds, you should work with a tax professional to make sure you're capturing the full benefit.
When are estimated quarterly taxes due?
The IRS runs on a four-quarter tax rhythm. However, the agency shares deadlines and dates that you should be aware of if you’re a small business or self-employed professional.
For 2025 taxes, here's the schedule with the income periods each payment covers:
Q1 payment: April 15 (covers January 1 – March 31 income)
Q2 payment: June 16 (covers April 1 – May 31 income)
Q3 payment: September 15 (covers June 1 – August 31 income)
Q4 payment: January 15, 2026 (covers September 1 – December 31 income)
When a deadline falls on a weekend or federal holiday, it shifts to the next business day. The IRS date-stamps electronic payments when you submit, not when they process. Miss a deadline by even a day and the penalties start accruing immediately.
To stay on track, we recommend setting calendar alerts one week before each deadline, so you have sufficient time to review your numbers and submit. You can also schedule all four payments at once (if your cash flow plan allows it) and let future-you focus on running the business instead of racing the clock.
How to pay quarterly taxes online
You've done the math, set aside the money, and now it's time to send it to the IRS. Here are three ways you can pay your quarterly taxes online:
IRS Direct Pay
The Electronic Federal Tax Payment System (EFTPS)
Authorized debit/credit card processor
Let’s review how each one works.
1. Use IRS Direct Pay for fast payments
IRS Direct Pay keeps it simple with one form, no accounts to create, no passwords to remember.
Here's the process for paying quarterly taxes online via IRS Direct pay:
Go to IRS.gov/payments and choose "Direct Pay"
Select "Estimated Tax" and "1040-ES," then pick the correct tax year
Verify your identity with details from your last return (name, address, filing status, and SSN)
Enter the amount you owe plus your bank's routing and account numbers
Schedule the withdrawal (today or any date up to a year out) and authorize the payment
Save the confirmation number; you'll need it to modify or cancel
Ensure you double-check the tax year and SSN before submitting. Most Direct Pay errors stem from these two mistakes. You can also schedule multiple future payments in one session, but you'll need to set specific dollar amounts for each. Therefore, most business owners prefer to schedule one quarter at a time (as they calculate what they actually owe) when using IRS Direct Pay.
2. Pay online with EFTPS to manage taxes across businesses
The Electronic Federal Tax Payment System (EFTPS) works better when you're managing ongoing tax obligations across multiple quarters or multiple businesses. Unlike Direct Pay's transaction-by-transaction approach, EFTPS functions as a tax payment dashboard where you can schedule, modify, and track everything in one place.
Here is how to set up EFTPS to pay your quarterly taxes:
Start enrollment at EFTPS.gov with your SSN/EIN, bank routing number, and account number.
Wait for the US Treasury to mail you a PIN (usually takes about seven business days).
Use that PIN to create a password and enable multi-factor authentication.
Once you're in, you can schedule quarterly payments for the entire year, change or cancel amounts up to two days before processing, and access 16 months of payment history that you can export for your records.
The history feature on EFTPS is particularly valuable during tax season when you need to verify exactly what you paid and when.
The trade-off: you’ll have to wait the initial seven days for a PIN and deal with an interface that's functional but outdated compared to modern banking apps.
3. Use a Debit or Credit Card when a transfer isn’t possible
The IRS links to two authorized processors: Pay1040 and ACI Payments. To pay, you enter your tax details, credit card information , and get instant confirmation. This is convenient when you're racing a deadline, but keep in mind you’ll pay credit card fees.
Debit cards carry a small flat fee (typically $2 to $3), while credit cards get charged a 1.85 to 2.50% of the payment amount ( which usually exceeds any rewards points you'd earn). Card payments are a good option only when bank transfers aren't available or if you need to spread your tax payments over a billing cycle. If you use them every quarter, those convenience fees add up fast.
If you do end up paying with a card, ensure you save the confirmation number before closing your browser. Lots of processors display it on-screen, but most don't email it automatically. You'll need that number if you need to verify the payment later or resolve any issues with the IRS.
How Relay simplifies quarterly tax payments
Picture this: you open your banking app and see exactly how much you've saved for taxes—no spreadsheets, no guessing. With Relay, you can create a dedicated tax account (one of 20 checking accounts available with no minimum account balances) and set up an automatic rule that moves 25 to 30% of every deposit straight into it.
This separation keeps your finances clear: operating cash in one (or more) accounts and tax reserves in another. This gives visibility into what's actually available for hiring, equipment, or growth because committed tax money isn't mixed in with your working capital.
When quarterly deadlines arrive, you can log into IRS Direct Pay or EFTPS and pay directly from your Relay tax account or use your Relay card if you prefer card payments.
Plus, everything syncs to QuickBooks Online or Xero. Now, you can see the payment categorized correctly without manual entry. And you can approve transactions, check balances, and adjust transfer rules from your phone.
With Relay, you get an automated organization system that makes quarterly taxes one less thing to track manually.
Relay is a financial technology company and is not an FDIC-insured bank. Banking services provided by Thread Bank, Member FDIC. Certain conditions must be satisfied for pass-through deposit insurance coverage to apply. The Relay Visa® Debit Card is issued by Thread Bank, member FDIC, pursuant to a license from Visa U.S.A. Inc. and may be used anywhere Visa debit cards are accepted. The Relay Visa Credit® Card is issued by Thread Bank, Member FDIC, pursuant to a license from Visa U.S.A. Inc and may be used anywhere Visa credit cards are accepted.
Conclusion and next steps
We’ve covered the three ways to pay quarterly taxes online: Direct Pay, EFTPS, and card payments. Now, it’s time to be proactive. Set up your system by creating a dedicated tax account and automating 25 to 30% transfers from every deposit.
Afterwards, you can calculate your Q1 payment using the safe-harbor method we mentioned earlier, schedule it through Direct Pay or EFTPS or set reminders for the remaining quarters. Make this the year quarterly taxes stop being a headache.
Relay is a financial technology company and is not an FDIC-insured bank. Banking services provided by Thread Bank, Member FDIC. FDIC deposit insurance covers the failure of an insured bank. Certain conditions must be satisfied for pass-through deposit insurance coverage to apply. The Relay Visa® Debit Card is issued by Thread Bank, member FDIC, pursuant to a license from Visa U.S.A. Inc. and may be used anywhere Visa debit cards are accepted. The Relay Visa Credit® Card is issued by Thread Bank, Member FDIC, pursuant to a license from Visa U.S.A. Inc and may be used anywhere Visa credit cards are accepted. Certain conditions must be satisfied for pass-through deposit insurance coverage to apply.
