How to Perform Payroll in QuickBooks

Learn the differences between the detail and summary methods for manually entering payroll into QuickBooks Online.
Seth DavidDec 9, 2020

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There are two ways to manually enter payroll in QuickBooks Online if your payroll software product doesn't integrate with it. Which method you choose will depend on how much detail you want in your payroll reports within QuickBooks Online. Before we get into the two methods, you need to understand the basics, as well as the most common mistakes inexperienced bookkeepers make while entering payroll.

Payroll basics

Let’s assume that all employees are being paid via direct deposit. Your payroll service will take out three payments with each payroll:

  • Net pay

  • Taxes

  • Fees

Many bookkeepers make the mistake of simply bookkeeping the net pay to payroll expense and the taxes to the employer tax expense.

Here’s what they should be instead:

Net pay: Net pay is comprised of the gross pay, which is the true expense to the company, less the withholding. The withholding amounts belong to the government. So they are deducted from the employee’s paycheck and placed in a liability account. That liability is cleared out when the tax payment is made.

Taxes: The tax payment is made up of two parts, which means the transaction needs to be split. Part of the payroll tax payment is the withholding that came from the employees’ paychecks. The other part is the employer’s share of the taxes. Most of the employer’s taxes come from matching Social Security and Medicare tax.

The payment of the withholding is what zeros out with the payroll liabilities. The employer’s share of the taxes is an expense that goes on the income statement, along with the gross payroll expense. They each go on separate lines.

Fees: The fees simply get booked to a payroll fees expense account.

Officer’s salaries: The other thing worth noting here is that if your company is an S Corp, then you need to break out the officer’s salaries on a separate line on the income statement.

The two methods for entering payroll

The summary method

As long as you understand the above first, then this next part should be fairly easy to follow.

Most companies will want to book the payroll as a summary. In other words, you would book each of the three transactions described above as a lump sum.

The gross pay would be the total gross pay for all employees. Same for the withholding. Then the net pay comes out and matches exactly what comes out of the bank account.

For payroll in QuickBooks Online, you record a check for this and everything reconciles just fine.

The tax payment is split based on the total withholding for all employees, and the total employer match. Again you write a check in QuickBooks Online with the split between the payroll liabilities and employer taxes, and everything should reconcile.

The detail method

This method is for reporting enthusiasts like me who want it all. I want each paycheck recorded separately, with each employee as a payee. The other situation when you need this is if your payroll company doesn’t pull the funds out of your bank, as I described above. I’ve seen two services that take out the funds in a strange way.

In the detailed method, you record each individual paycheck in the exact manner described above. Instead of recording them as checks in your bank account, you will set up a new bank account in QuickBooks Online. Call it “Payroll Clearing.”

When you record the paychecks in the Payroll Clearing account, you still book the gross pay and the withholding. The balance in the Payroll Clearing account will be negative. When all of the paychecks are in, that negative amount should be exactly equal to the amount of the net pay that comes out of the bank account. When that transaction is posted in the bank account, book it to the Payroll Clearing. That will zero out the payroll clearing.

Book the taxes and fees the same way as above.

The video above demonstrates how all of this works. My sample report is can be found here.

Payroll is normally the biggest expense that a company has. This makes it that much more important to book it correctly.

Not sure if your books are correct? Check your payroll entries in QuickBooks Online. Even if you don’t understand the accounting side of things, the giveaway is that the payroll checks should be split between gross pay and liabilities. If you see the split, it means that your bookkeeper probably knows what they’re doing.

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A version of this article was first published on Fundera, a subsidiary of NerdWallet