When it comes time to pay your federal estimated quarterly taxes, you have 2 choices:

  • Mail payments. This option is free. We help you fill out a voucher—1040-ES—and tell you how to mail it.
  • Make payments online. If you upgrade to our Tax Bundle, you can make payments online directly from within our product.

Making payments online

The ability to pay your quarterly estimated taxes online through EFTPS requires the tax bundle. In order to set it up, you need to first enroll at eftps.gov using your Social Security number. Be sure to enroll as an Individual. Don’t use an EIN or enroll as a Business. It can take a few weeks to receive your PIN from EFTPS, so be sure to give yourself enough time.

Once you've enrolled with EFTPS and received your pin, it's time to set up online payments:

  1. Log into QuickBooks Self-Employed and go to the Quarterly Taxes page
  2. Select Pay Now in the upper right corner
  3. Select Online
  4. Enter your details from EFTPS and select either the current or a unique amount
  5. Press continue and follow the onscreen prompts
The payment should reflect in QuickBooks Self-Employed as pending on the Quarterly Taxes page. Once the payment has cleared with your bank, it will update.

Making payments outside of QuickBooks Self-Employed

If you are paying by mail or through another source, you need to make sure the transaction is recorded as Estimated Taxes on the Transactions page. If you have connected the bank account from which the payment is being made, then simply wait for the transaction to download into QuickBooks Self-Employed and categorize it as Estimated Taxes. Otherwise, you will need to manually create the transaction.

Don't see the payment reflecting for the quarter? You can then ensure the transaction is assigned to the right quarter by following these steps:

  1. Go to Taxes then Quarterly Taxes
  2. Select the quarter you want the mark the tax payment for
  3. Click on "Don't see your payment? Find your estimated tax payments"
  4. Check off the tax payment and select "mark as tax payment"
Tip! If you see the payment under "paid estimated taxes" no further action is needed. Be sure to double check the date the transaction cleared! It may not have cleared your bank and pulled into QuickBooks Self-Employed until after the quarter ended.