How to Do Payroll in California for Small Businesses

If you’re just starting a business in California and expecting to hire employees, you’ll soon need to tackle the challenge of payroll. Managing payroll can be tricky, so it’s important to have a thorough understanding of the processes before you begin. 

Lucky for you, this guide lays out all the steps for successful payroll processing in California. 

1. Get an EIN

Your Employer Identification Number, or EIN, is like a social security number for your company, enabling the IRS to identify your business. It is also known as a Federal Tax Identification Number (FTIN), or sometimes for corporations just Tax Identification Number (TIN). 

An EIN is used to identify US businesses and the taxpayers required to file the relevant tax returns. The EIN also contains information about the state in which the company is registered. 

Employers use their EIN to file taxes, so in order to process payroll and ensure the proper withholdings and tax payments, you’ll need to first obtain your EIN. The application is free and can be found on the IRS website. 

The application is form SS-4, and it can be printed out and mailed to the IRS, or submitted electronically. Once your information on the application has been validated, your EIN is assigned immediately. The EIN will never expire and is never duplicated, even if you go out of business.

In California, you’ll also need to register for state withholdings with the California Employment Development Department. This will also register your business for state unemployment taxes (SUTA) and other payroll taxes.

Your municipality may also require certain tax registrations, so check with your local government for requirements.

2. Employee Tax Information

You’ll need to collect several forms from your employees, starting with a W-4 and an I-9 for all W-2 employees. In California, your employee will also need to fill out this form to enable tax withholding. You may also need to register with your city and municipality, so check with your local governments for the required forms. 

These forms are necessary to withhold taxes from payroll checks and must be kept on file. They are not submitted to the IRS or the state. You’ll also need these forms to issue W-2s, or in the case of independent contractors, 1099s. 

If you plan to pay employees by direct deposit, you’ll need to collect their bank information, including account and routing number, address, and phone number. You’ll also need an Automated Clearing House (ACH) account with your bank in order to make direct deposits. An ACH account allows you to transfer payroll funds to your employees’ bank accounts.

3. Establish Your Payroll Schedule

In California, payment frequency requirements are as follows:

In California, wages must be paid at least twice during each calendar month on the days designated in advance as regular paydays. The employer must establish a regular payday and is required to post a notice that shows the day, time and location of payment. 

Labor Code Section 207 Wages earned between the 1st and 15th days, inclusive, of any calendar month must be paid no later than the 26th day of the month during which the labor was performed, and wages earned between the 16th and last day of the month must be paid by the 10th day of the following month. 

Other payroll periods such as weekly, biweekly (every two weeks) or semimonthly (twice per month) when the earning period is something other than between the 1st and 15th, and 16th and last day of the month, must be paid within seven calendar days of the end of the payroll period within which the wages were earned. Labor Code Section 204.

You can choose to pay your employees more often, such as weekly, as long as you meet state requirements. 

4. Calculate Gross Pay

If you have salaried employees, gross pay is simply their contracted fixed pay amount, such as $2,000 per week. For hourly employees, calculating gross pay is easy. 

First, review their timesheets to make sure they have accurately tracked their hours. Then simply multiply their hours for that week, or month, by their hourly rate. 

For example, if Jane works 40 hours in a week at $15 per hour, her gross pay (40 x 15) is $600. 

Keep in mind that in California, there are overtime requirements. You must pay:

• One and one-half times the employee’s regular rate of pay for all hours worked in excess of eight hours up to and including 12 hours in any workday, and for the first eight hours worked on the seventh consecutive day of work in a work week; and
• Double the employee’s regular rate of pay for all hours worked in excess of 12 hours in any workday and for all hours worked in excess of eight on the seventh consecutive day of work in a work week.

If you fail to pay your employees the correct overtime rate, your business could face serious fines and other penalties, and be required to back pay the unpaid overtime.

To calculate overtime pay, take the number of hours over 40 in a work week, 8 or 12 hours in a day, and multiply it by their hourly overtime pay rate.

So if Jane worked 10 regular overtime hours at $22.50 ($15 x 1.5), she’d be owed (10 x 22.5) $225. If she also worked a 14-hour day, she’d be owed two hours at two times her regular pay, which would be $30 ($15 x 2) x 2, or $60. 

Adding in her normal hours, Jane’s total gross pay for that week would be $600 + $225 + $60  = $885.

These calculations can be easily done in a spreadsheet, which should then be kept in your records in case any pay disputes arise. 

5. Determine Withholdings, Deductions, and Allowances

Exemptions are the same as allowances — both refer to the money taken out of an employee’s paycheck. Allowances are specified on the employee’s W-4. 

Payroll deductions, which are specified by the employee on their tax returns, are amounts that can be deducted from taxable income. When determining withholding amounts, you’ll need to refer to your employees’ tax forms, and be sure they filled them out correctly. 

Deductions may include the following:

• Federal taxes
• Social Security
• State taxes
• Local taxes
• Medicare
• 401(k) contributions
• Workers’ compensation contribution
• Unemployment withholding
• Other benefits, such as company-subsidized health insurance

Jane, for instance, might pay $130 in federal taxes, $15 in social security, and $40 in state taxes, in addition to $30 in 401(k). Thus, her total withholdings would be $215. 

Again, it’s a good idea to use a spreadsheet to record the totals for each employee, as it makes calculating and remembering much easier.  

To calculate federal income tax withholdings, you’ll need to refer to IRS Publication 15. You can find information on withholding California taxes here. 

In California, employees also pay State Disability Insurance (SDI) taxes, so those need to be withheld as well. 

6. Calculate Net Pay

To calculate net pay, simply deduct withholdings from the gross pay you previously calculated.

Gross pay – Withholdings = Net pay

So, Jane’s net pay for the week detailed above would be $885 minus $275, which equals $615.

7. Pay Employees

To offer direct deposit, you’ll need to first set up an ACH account with your bank, which will require a business bank account. You can usually set it up online following your bank’s instructions. Once your account is set up, you’ll add your employees as payees. 

Then, you’ll process the ACH payments through your bank and provide every employee with a pay stub detailing itemized withholdings. This also applies if you issue paper checks. 

8. Keep Records

It’s important to keep detailed payroll records, which can be used in the event of an error or dispute. You’ll also need these records to calculate your own payroll tax payments. 

If you do your own payroll and tax calculations by hand, you’ll want to keep ledgers of everything you withhold and pay. But keep in mind that most accounting software tools, like QuickBooks or Freshbooks, incorporate payroll accounting capabilities and will do all this work for you. 

If you’re just starting your business and planning to do your own accounting and payroll, you may want to consider purchasing some quality accounting software. It will not only save you a great deal of time, but ensure error-free payroll and tax calculations. 

9. Pay Federal Payroll Taxes

Following IRS guidelines for depositing withheld taxes and paying your payroll taxes is absolutely crucial. Here are the instructions from the IRS website:

Depositing Employment Taxes

In general, you must deposit federal income tax withheld as well as employer and employee social security and Medicare taxes.

There are two deposit schedules, monthly and semi-weekly. Before the beginning of each calendar year, you must determine which of the two deposit schedules you are required to use. To determine your payment schedule, review Publication 15 for Forms 941, 944 and 945. For Form 943, review Publication 51.

Deposits for FUTA Tax (Form 940) are required for the quarter within which the tax due exceeds $500. The tax must be deposited by the end of the month following the end of the quarter.

You must use electronic funds transfer (EFTPS) to make all federal tax deposits. See the Employment Tax Due Dates page for information on when deposits are due. If you fail to make a timely deposit, then you may be subject to a failure-to-deposit penalty of up to 15 percent.

Reporting Employment Taxes

Generally, employers must report wages, tips and other compensation paid to an employee by filing the required form(s) to the IRS. You must also report taxes you deposit by filing Forms 941, 943, 944, 945, and 940 on paper or through e-file.

Federal Income Tax and Social Security and Medicare Tax

In general, employers who withhold federal income tax, social security or Medicare taxes must file Form 941, Employer’s Quarterly Federal Tax Return, each quarter. This includes withholding on sick pay and supplemental unemployment benefits.

File Form 943, Employer’s Annual Federal Tax Return for Agricultural Employees, if you are filing to report agricultural wages.

File Form 944, Employer’s Annual Federal Tax Return, if you have received written notification about the Form 944 program.

File Form 945, Annual Return of Withheld Federal Income Tax, if you are filing to report backup withholding.

Federal Unemployment Tax Act (FUTA)

Only the employer pays FUTA tax and it is not withheld from the employee’s wages. Report your FUTA taxes by filing Form 940, Employer’s Annual Federal Unemployment (FUTA) Tax Return.

10. Pay California Payroll Taxes

In California, payroll taxes are a bit complicated. 

Employers contribute to:

• Unemployment Insurance (UI)
• Employment Training Tax (ETT)

       Employees pay into state payroll taxes with wage withholdings for:

• State Disability Insurance (SDI)
• Personal Income Tax (PIT)

You can pay all your taxes through your account on the Economic Development Department website. 

Again, be sure to check with your local government to find out about any local payroll taxes. 

Using a Payroll Service

Processing payroll can be quite complex, so you might want to consider using a payroll service. It’s likely to be less expensive than creating a new staff position for managing payroll. 

Payroll and payroll taxes come with countless laws, rules and restrictions, and a payroll service can ensure your business remains in compliance at the federal, state and local levels. 

With a payroll service, all you need to do is send your digital timesheets and relevant employee and business information, and all the calculations will be made for you. The service will take care of payments as well, freeing you up to focus on running, and growing, your business. 

We highly recommend hiring a payroll service — as a busy entrepreneur, you won’t regret it!