How To Pay Payroll Liabilities In Quickbooks Online

Running payroll comes with the responsibility of properly paying payroll taxes and filings to avoid penalties. If you use QuickBooks Online to run payroll for your small business, here are some tips to ensure you stay compliant with payroll liabilities.

If you’re short on time, here’s a quick answer to your question: You can pay payroll liabilities in QuickBooks Online by setting up tax payments, enabling auto-pay for payroll taxes, paying taxes manually through the Pay Liabilities screen, or authorizing QuickBooks Payroll to make tax payments on your behalf through Full Service Payroll.

In this comprehensive guide, we will cover everything you need to know about paying payroll tax liabilities in QuickBooks Online, including an overview of payroll liabilities, how to set up tax payments, paying manually vs. auto-pay, using Full Service Payroll, and some best practices to avoid penalties.

What are payroll liabilities?

Payroll liabilities refer to the various taxes and deductions that employers are responsible for withholding from their employees’ paychecks and remitting to the appropriate government agencies. These liabilities include federal income tax withholding, Social Security and Medicare taxes, and federal and state unemployment taxes.

Federal income tax withholding

When an employee is paid, their employer is required to withhold a certain amount of their wages for federal income taxes. The amount withheld is based on the employee’s Form W-4 and the tax withholding tables provided by the Internal Revenue Service (IRS).

Employers are responsible for accurately calculating and remitting these withheld taxes to the IRS on behalf of their employees.

Social Security and Medicare taxes

Employers are also responsible for withholding and remitting Social Security and Medicare taxes, commonly referred to as FICA taxes, from their employees’ paychecks. These taxes fund the Social Security and Medicare programs and are calculated as a percentage of an employee’s wages.

In 2021, the Social Security tax rate is 6.2% and the Medicare tax rate is 1.45%. Employers are required to match these amounts and remit them to the appropriate government agencies.

Federal and state unemployment taxes

In addition to income and FICA taxes, employers are also responsible for paying federal and state unemployment taxes. These taxes fund unemployment compensation programs and are used to provide benefits to eligible workers who become unemployed.

The rates for these taxes vary depending on factors such as the employer’s industry and the state in which they operate. It is important for employers to accurately calculate and remit these taxes to avoid penalties and ensure compliance with tax regulations.

For more detailed information on payroll liabilities and how to handle them in QuickBooks Online, you can visit the QuickBooks Resource Center.

How to set up tax payments in QuickBooks Online

Setting up tax payments in QuickBooks Online is an essential step in managing your payroll liabilities efficiently. By following these simple steps, you can ensure that your tax payments are accurate and made on time.

Enabling tax agencies in QuickBooks Online

The first step in setting up tax payments is to enable tax agencies in QuickBooks Online. This allows you to track and pay your payroll liabilities directly from the software. To do this, navigate to the “Taxes” tab in QuickBooks Online and select “Set up tax agencies.”

From there, you can add the tax agencies relevant to your business and input the necessary information, such as tax ID numbers and filing frequencies.

Connecting bank accounts

Once you have enabled tax agencies, the next step is to connect your bank accounts to QuickBooks Online. This allows for seamless payment processing and ensures that your tax payments are deducted directly from your bank account.

To connect your bank accounts, go to the “Banking” tab in QuickBooks Online and select “Connect account.” Follow the prompts to link your bank accounts securely.

Setting up auto-pay (optional)

QuickBooks Online also offers the option to set up auto-pay for your tax payments. This feature automatically deducts your payroll liabilities from your bank account on the due date, saving you time and eliminating the risk of late payments.

To set up auto-pay, go to the “Taxes” tab in QuickBooks Online and select “Payroll settings.” From there, you can enable auto-pay and customize the payment settings to fit your needs.

By following these steps, you can easily set up tax payments in QuickBooks Online and streamline your payroll process. Remember to review your tax payments regularly to ensure accuracy and make any necessary adjustments.

With QuickBooks Online’s user-friendly interface and robust features, managing your payroll liabilities has never been easier.

Manually paying taxes in QuickBooks Online

When it comes to paying payroll liabilities in QuickBooks Online, you have the option to manually pay your taxes. This allows you to have more control over the process and ensures that your payments are accurate and on time.

Here is a step-by-step guide on how to manually pay your taxes in QuickBooks Online:

Navigating to the Pay Liabilities page

To get started, navigate to the Pay Liabilities page in QuickBooks Online. This can be done by going to the Taxes tab and clicking on “Payroll Tax” or “Pay Liabilities.” Once you are on the Pay Liabilities page, you will see a list of your tax liabilities that need to be paid.

Selecting tax agencies to pay

On the Pay Liabilities page, you will see a list of your tax liabilities, including federal and state taxes, as well as other payroll liabilities such as health insurance contributions or retirement plans.

To manually pay your taxes, select the tax agencies you want to pay by checking the boxes next to their names.

Specifying payment date and amount

After selecting the tax agencies you want to pay, specify the payment date and amount. QuickBooks Online will automatically calculate the amount you owe based on your payroll data. Make sure to double-check the figures to ensure accuracy.

You can also add any additional notes or memos regarding the payment if necessary.

Paying electronically or by check

Once you have specified the payment details, you have the option to pay electronically or by check. QuickBooks Online allows you to pay electronically through the Electronic Funds Transfer (EFT) service. This is a convenient and secure way to make your tax payments directly from your bank account.

Alternatively, you can choose to print a check and mail it to the tax agencies.

It is important to note that when paying electronically, you may be required to enroll in the EFTPS (Electronic Federal Tax Payment System) for federal tax payments. This is to ensure compliance with IRS regulations. QuickBooks Online will guide you through the enrollment process if necessary.

By following these steps, you can easily manually pay your taxes in QuickBooks Online. Remember to keep track of your payment receipts and reconcile them with your payroll records to maintain accurate financial records.

For more detailed information and step-by-step instructions, you can refer to the official QuickBooks Online Help Center:

Using Full Service Payroll for tax payments

When it comes to paying payroll liabilities in QuickBooks Online, one efficient option is to use the Full Service Payroll feature. Full Service Payroll offers a convenient way to handle your tax payments and ensure that you meet all your obligations as an employer.

This feature streamlines the process and saves you valuable time.

How Full Service Payroll works

Full Service Payroll in QuickBooks Online takes care of calculating and filing your payroll taxes for you. It automatically deducts the necessary amounts from your employees’ paychecks and sets them aside to cover your tax liabilities.

Once the calculations are done, QuickBooks Online generates the necessary tax forms and reports, making it easy for you to stay compliant with tax regulations.

With Full Service Payroll, you can rest assured that your payroll taxes are accurate and up to date. The feature automatically keeps track of any changes in tax rates or regulations, ensuring that you are always in compliance.

Authorizing QuickBooks to make tax payments

Before QuickBooks can make tax payments on your behalf, you need to authorize the software to do so. This involves providing your bank account information and granting QuickBooks the necessary permissions to debit your account for tax payments.

Once you have authorized QuickBooks to make tax payments, the software will take care of the rest. It will automatically initiate the payments on the due dates, ensuring that you meet your tax obligations on time.

This feature eliminates the need for manual payments and reduces the risk of missing deadlines.

Deadlines for authorizing payments

It’s important to note that there are specific deadlines for authorizing tax payments in QuickBooks Full Service Payroll. These deadlines vary depending on the type of tax and the frequency of your payroll schedule.

To ensure that your tax payments are made on time, it is recommended to authorize payments at least a few days before the due date. This allows for any potential processing delays and gives you peace of mind knowing that your tax obligations are being met.

Best practices to avoid penalties

When it comes to paying payroll liabilities in QuickBooks Online, it is important to follow best practices to avoid penalties. Here are some tips to help you stay on top of your payments:

Pay on time

One of the most important things you can do to avoid penalties is to pay your payroll liabilities on time. Ensure that you are aware of the due dates for your payments and make sure to submit them before the deadline.

This will help you avoid any late fees or penalties that may be imposed by tax authorities.

Double check payment amounts

Another best practice is to double check the payment amounts before submitting them. It is important to ensure that you are paying the correct amount for each liability. Mistakes in payment amounts can lead to discrepancies and may result in penalties.

Take the time to review the numbers and verify that they are accurate.

Sign up for reminders

QuickBooks Online offers a useful feature that allows you to sign up for reminders. By enabling this feature, you will receive notifications and reminders about upcoming payroll liabilities and their due dates. This can be a helpful tool to keep you organized and ensure that you never miss a payment.

Consult a tax expert if unsure

If you are unsure about any aspect of your payroll liabilities or have questions regarding tax regulations, it is always a good idea to consult with a tax expert. They can provide you with guidance and ensure that you are following the correct procedures.

It is better to seek professional advice than to risk making mistakes that could lead to penalties.

By following these best practices, you can avoid penalties and ensure that your payroll liabilities are paid accurately and on time. Remember, staying organized and staying informed are key to successfully managing your payroll in QuickBooks Online.


Handling payroll taxes properly is crucial for remaining compliant and avoiding costly penalties. QuickBooks Online provides flexible options to pay your payroll liabilities seamlessly.

Setting up tax payments correctly from the start, enabling auto-pay, double checking amounts, and paying on time will help you stay on top of your payroll tax obligations. Don’t hesitate to consult with a tax professional if you need help navigating state and federal payroll regulations.

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