Auto Payroll Taxes

The short answer is that QuickBooks calculates your federal and state payroll taxes automatically every time you run payroll, but it does not pay them automatically unless you have enrolled in Intuit's e-pay and e-file services (or, for some users, the enhanced autopayroll tax payment feature). Without that enrollment, you or your bookkeeper still need to initiate the payment manually by the agency deadline.

In QuickBooks Online Payroll, go to Settings > Payroll Settings and look under the Taxes section. You will see options for Electronic Services, where you can add your bank account and set up e-pay for federal and state tax agencies. Once that is active, you can choose to have QuickBooks auto-pay supported taxes on their due dates. If you do not see that option, your payroll subscription tier may not include it, or your state may not yet be supported for e-pay.

In QuickBooks Desktop with Enhanced Payroll, open the Employees menu and choose Payroll Center. Under the Pay Liabilities tab, select Change Payment Method and follow the prompts to enroll in e-pay. After enrollment, you can set individual tax schedules to pay electronically, but Desktop Enhanced still requires you to click to submit each payment -- it does not fully auto-pay on its own. Full Service payroll handles filings and payments for you as part of the service.

One common pitpitfall: even with e-pay active, if your bank account on file has insufficient funds or a tax agency sends a new rate notice that has not been updated in QuickBooks, the auto-payment can fail or calculate incorrectly. Our engineers recommend reviewing the Payroll Tax Liabilities report at least once a quarter to confirm every liability shows a scheduled (or completed) payment, and updating any new state unemployment or withholding rates as soon as the notice arrives.

Nope, they just changed this July 1st to them auto paying without the ability to opt out.  FYI I own my own business and am my own accountant.