Get a federal Employer Identification Number if you don’t have one. Apply through the IRS website and you’ll receive it immediately. This number is required before you can register with state agencies or run payroll.

Register with your state’s tax and employment agencies. In California, this means setting up an account with the Employment Development Department. You’ll receive an employer account number for reporting wages and paying state taxes. Most states have a similar process through their department of revenue or labor department.

Understand what you’re required to withhold. Federal income tax and Social Security and Medicare taxes apply everywhere. California adds state income tax, State Disability Insurance, and Paid Family Leave withholding. As the employer, you also pay unemployment insurance and employment training tax. Get the withholding amounts wrong and your employees get surprised at tax time or you face penalties.

Collect the right paperwork from employees before their first paycheck. Every employee needs to complete a W-4 for federal withholding and an I-9 to verify work eligibility. California requires a separate DE 4 form for state withholding if the employee wants different allowances than their federal W-4.

Choose how you’ll process payroll. Manual calculation works but leaves room for error and requires you to handle tax deposits and quarterly filings yourself. Payroll software like Gusto or QuickBooks Payroll automates calculations and filings for a monthly fee. Payroll setup and training from a professional can help you configure the system correctly from the start and avoid costly mistakes.

Set up your deposit schedule. Federal payroll taxes typically deposit monthly or semi-weekly depending on your total tax liability. California requires quarterly or monthly deposits based on the amount you withhold. Missing deposit deadlines triggers penalties immediately.

Get workers’ compensation insurance before your first employee starts. California requires it for all employers with few exceptions. Your premium depends on your industry classification and payroll size.

File quarterly reports with the IRS and your state. Form 941 reports federal wages and taxes. California requires quarterly wage reports through the EDD. At year end, you’ll also prepare W-2s for employees and file annual reconciliation reports.

The initial setup takes some effort, but the ongoing work is manageable once your systems are in place. Many San Diego small business owners handle payroll themselves with the right software. Others outsource it entirely because the cost of professional help is less than the time and stress of doing it wrong.