1. Know what QuickBooks tracks versus what it files. QuickBooks keeps your books: income, expenses, payroll, sales tax collected. None of that is itself a tax return. Filing happens as a separate step, outside QuickBooks, done by you, your accountant, or another piece of software using QuickBooks' numbers as its input.
2. Hand your accountant access or a report, not a login to file for you. Most businesses get their income taxes filed by giving their accountant QuickBooks access, or exported reports like Profit and Loss and Balance Sheet, and letting them prepare and file the actual return entirely outside QuickBooks.
3. If you're self-employed, QuickBooks Self-Employed can hand off straight to TurboTax. It has a bundle option with TurboTax Self-Employed; your categorized transactions flow into TurboTax so you're not re-entering them, and TurboTax is what actually calculates and files the return.
4. Quarterly estimated taxes work the same way, through that same TurboTax connection. QuickBooks Self-Employed estimates what you owe each quarter based on your income and expenses, but TurboTax, or your own filing, is still what actually submits the payment.
5. Payroll tax forms are the real exception. On a QuickBooks Online Payroll plan that includes tax filing (Core, Premium, or Elite), QuickBooks does prepare and e-file your federal and state payroll tax forms, like Form 941, on schedule, without you filing them separately. Sales tax gets calculated and tracked for you too, though whether QuickBooks actually submits the return or just hands you the number depends on your state and setup.