QuickBooks

How to Pay Quarterly Taxes in QuickBooks (and Why the Answer Depends on Which One You Use)

QuickBooks Self-Employed calculates your estimated quarterly tax payment automatically under its Taxes tab. QuickBooks Online and Desktop don't do this for a regular business: neither one estimates self-employment or income tax at all, so you or your accountant work out the number yourselves and just record the payment as a transaction once it's made.

The full walkthrough

1. Start by pinning down which QuickBooks product you're actually on. That decides everything else here. QuickBooks Self-Employed (QBSE) is built for sole proprietors filing a Schedule C and has a built-in quarterly tax estimator. QuickBooks Online and Desktop, the versions most small businesses run, don't estimate income tax or self-employment tax, no matter how complete your books are.

2. On QuickBooks Self-Employed, open the Taxes tab and select Quarterly. You'll see the estimated payment for the current quarter, calculated from your categorized income, expenses, and mileage. Keep your transactions reviewed through the quarter, since the estimate is only as good as the data behind it.

3. Check the due date and pay it. QBSE shows the amount and the deadline. You can pay directly from the app once you've enrolled in e-pay through EFTPS, or take the number it gives you and pay through IRS Direct Pay or by mailing a check with the 1040-ES voucher.

4. On QuickBooks Online or Desktop, skip the estimate and go to your accountant or a 1040-ES worksheet instead. Neither product has anything resembling QBSE's Quarterly tab. The number has to come from outside QuickBooks entirely.

5. Make the payment outside QuickBooks. Pay through IRS Direct Pay, EFTPS, or mail a check, the same options available to QBSE users who haven't set up in-app e-pay.

6. Record the payment as a transaction once it's made. Enter it as a check or expense so your books reflect the cash leaving the business. Most accountants book it to an owner's draw or equity account rather than a tax expense line, since income tax on a pass-through business's profit is personal, not a deductible expense; a C corp's own tax liability works differently. Check with your accountant on which applies to you.

Where the estimate, or the lack of one, causes problems

The real pain point isn't remembering to open QuickBooks four times a year. It's that income rarely arrives evenly, so a flat guess based on last quarter is often wrong by the time the next one's due, leading to either an underpayment penalty or a payment big enough to strain cash flow for the quarter it comes out of.

For a growing or seasonal business, this gets worse fast. A strong third quarter means the fourth quarter's payment should probably be higher too, but nothing is watching that number change as it happens unless someone's actively recalculating it, and on QBO or Desktop there's nothing even producing a first draft to start from.

What we've built on top of QuickBooks quarterly taxes

A running estimate that updates as income comes in

Instead of a stale number calculated once a quarter, income and expense data from bank feeds and invoicing feeds a running projection, so the upcoming payment estimate adjusts as the quarter actually unfolds, not just at the end of it.

A reminder tied to your actual calendar, not a sticky note

A due-date check flags the payment coming up and the latest estimate well ahead of time, instead of someone realizing on the 14th that the deadline is tomorrow.

What does your quarterly tax process actually look like right now?

Tell us whether you're guessing each quarter, using an accountant's worksheet, or something else entirely, and we'll tell you if the number can calculate itself.

Let's talk

Guessing at your quarterly tax number every few months?

Tell us how you currently land on the figure, a flat guess, last year's total divided by four, an actual recalculation, and we'll tell you if it can run off your real numbers automatically. Quarterly taxes are just one place QuickBooks leaves you to do the math yourself; if something else in your business is running on a guess instead of real data, bring that to us too.

Let's talk

Frequently Asked Questions

Does QuickBooks Online calculate my quarterly estimated taxes?+

No. QuickBooks Online tracks your income and expenses, but it doesn't estimate self-employment or income tax the way QuickBooks Self-Employed does. For a QBO business, that calculation comes from your accountant or a 1040-ES worksheet; QuickBooks just helps you record the payment once you know the number.

How do I file quarterly payroll taxes in QuickBooks?+

That's a different task from paying your own estimated income tax. Payroll tax deposits, the federal and state withholding and employer taxes tied to running payroll, are handled through QuickBooks Payroll's tax center, which calculates and can e-pay those amounts for you on a payroll plan. It has nothing to do with the owner's personal quarterly estimate.

What category should a quarterly tax payment go to in QuickBooks?+

For a sole proprietor, partner, or S corp owner, most accountants book it to an owner's draw or equity account rather than a tax expense, since income tax on your share of the profit is a personal obligation, not a deductible business expense. A C corp's own income tax is different and usually runs through a tax liability account. Confirm with your accountant since this affects your financial statements.

Can QuickBooks Self-Employed pay the IRS for me?+

Once you've enrolled in e-pay through EFTPS inside the app, yes, QBSE can submit the payment directly. If you haven't enrolled, you can still use the estimate it calculates and pay through IRS Direct Pay or by mail instead.