Payroll Companies & Payroll Services in San Diego, CA

Pay-Net is an independent payroll provider headquartered in San Diego, California. It works with employers in Southern California and in other states, combining payroll processing with HR tools, time tracking, tax filing and workers' compensation support. Its services are aimed at employers, not individual workers. Employees who have questions are referred back to their own employer's payroll or HR staff.

Background and Credentials

Wayne Lee and Don Fallon started the company in 1995, drawing on a combined 25 years of prior experience in payroll services. Fallon retired at the start of 2006 and Lee stepped away in April 2019. His son, Hollis Lee, now runs the business and is involved in its daily operations.

Pay-Net was a charter member of the Independent Payroll Providers Association (IPPA), which helps it keep its processing systems and its knowledge of federal and state payroll tax rules current. Since 2010, clients have entered payroll through Pay-Net Online, the firm's browser-based platform.

Payroll and Tax Capabilities

Clients can enter payroll in three ways: by importing data from a time system, by keying hours into a spreadsheet-style batch screen, or by editing one employee at a time. Settings can be applied to a whole company or to selected employee groups. Pay-Net offers both full and modified tax service, with agencies drafting tax payments directly. Year-end W-2s are produced, 1099s can be issued throughout the year, and electronic copies are available. Other payroll features include:

• Certified payroll, including prevailing wage reports and forms such as WH-347 and A-1-131
• Check options such as signed and sealed checks, direct deposit, manual checks, positive pay and on-site print-back
• Courier, FedEx or USPS delivery of payroll packages
• Labor distribution and job costing by job or cost center
• A large set of standard reports plus a custom report writer, general ledger output and portal access for outside CPAs and bookkeepers
• Union reports, retirement file transmission, child support and agency payments by check or ACH

HR, Time and Compliance Tools

Beyond processing pay, Pay-Net provides HR modules for administering benefits, including Section 125 plans, voluntary coverage, COBRA, 401(k) and IRA programs. Employers can also track licenses, certifications, training, leave, company assets and performance reviews, and can store custom documents. The time and attendance offering supports hardware clocks or web-based timekeeping, scheduling, coverage budgets, online timesheets and mobile management.

An employee portal included with time and attendance lets staff view pay stubs, pay history and W-2s, request time off and submit demographic changes. New hires can complete onboarding paperwork online, and E-Verify and state new hire reporting are handled automatically.

Insurance and Posting Compliance

Pay-Net reports payroll data to workers' compensation carriers, tracks liability and supports pay-as-you-go workers' comp arrangements. It coordinates with clients' insurance and benefit vendors and partners with local agency Amerson Lee. The company also sells laminated all-in-one federal and state labor law posters in English or Spanish.

Two monthly update subscriptions are available: one emails revised notices as they change, and the other mails a replacement poster set. Both include a fine-reimbursement guarantee. This mix suits employers that want payroll, HR administration and compliance support from one provider, including contractors that need prevailing wage reporting.