Get your registrations done before you touch QuickBooks. You need a federal Employer Identification Number from the IRS, a California employer account number from the EDD, and workers’ compensation insurance. If you’re going to withhold California state income tax, the EDD account covers that along with State Disability Insurance and Unemployment Insurance. Trying to set up payroll without these numbers wastes time because QuickBooks will stop and ask for them.

Pick a QuickBooks Online Payroll tier that matches what you need. Core handles full-service payroll with automated federal and state tax filings and direct deposit. Premium adds same-day direct deposit, HR support, and workers’ comp administration. Elite includes tax penalty protection and a dedicated setup expert. For most small businesses with a handful of employees, Core does the job.

Inside QuickBooks, start with the Payroll tab and run through the setup wizard. Enter your business legal name, address, EIN, and California EDD account number. Add your state tax rates, including your UI rate from the EDD notice you received when you registered. Connect the bank account you’ll use to fund payroll and pay tax deposits.

Add each employee one at a time. You’ll need their full legal name, address, Social Security number, W-4 withholdings, pay rate, and pay type (salary or hourly). For direct deposit, enter their bank routing and account numbers. Upload or record their I-9 and W-4 for your files. If you offer benefits like health insurance or a retirement plan, set up the deductions now so they apply from the first paycheck.

Set your pay schedule. Weekly, biweekly, semimonthly, and monthly are all options. Biweekly is the most common for California small businesses because it aligns well with overtime calculations under state wage and hour rules. Pick your first pay period start date and check date carefully, since QuickBooks uses those to drive tax deposit timing.

Run a test payroll before your first real one. Review the gross-to-net calculation, tax withholdings, and employer tax liability. QuickBooks calculates federal income tax, Social Security, Medicare, California state income tax, SDI, SUI, and ETT automatically. When the numbers look right, process it for real and QuickBooks will initiate direct deposits and schedule the tax deposits.

The setup is the hard part. Once employees and schedules are in place, running payroll takes a few minutes per cycle. If you’d rather not work through this yourself, payroll setup and training gets the system configured correctly from day one, including California-specific items like overtime rules, meal and rest period tracking, and proper pay stub formatting under Labor Code Section 226.

California has more payroll compliance landmines than most states, from sick leave accruals to final paycheck timing rules. Pasadena bookkeepers who work with California employers daily can help you avoid the mistakes that turn into EDD audits or wage claims down the road.