Payroll Specialist

The Payroll Specialist processes accurate and timely payroll for the organization’s employed staff and providers, ensuring compliance with wage‑and‑hour law, tax withholding, and benefit deduction requirements. This role serves as the organization’s designated Paychex administrator and is the primary point of contact with Paychex for all payroll, onboarding, termination, and system‑support matters. This position maintains payroll records, resolves discrepancies, and supports payroll-related reporting for Finance and Human Resources.

This role owns day‑to‑day payroll execution and Paychex system administration within established policy and requires comfort with independent decision‑making and working independently, while escalating for classification, deduction, or leave questions. Errors in this role can directly affect employee pay accuracy, tax compliance, and the organization’s regulatory standing.

The Payroll Specialist processes accurate and timely payroll for the organization’s employed staff and providers, ensuring compliance with wage-and-hour law, tax withholding, and benefit deduction requirements. This role serves as the organization’s designated Paychex administrator and is the primary point of contact with Paychex for all payroll, onboarding, termination, and system-support matters. This position maintains payroll records, resolves discrepancies, and supports payroll-related reporting for Finance and Human Resources.

This role owns day-to-day payroll execution and Paychex system administration within established policy and requires comfort with independent decision-making and working independently, while escalating for classification, deduction, or leave questions. Errors in this role can directly affect employee pay accuracy, tax compliance, and the organization’s regulatory standing.

• Processes bi-weekly payroll for all employees and providers, including hourly, salaried, and overtime calculations, ensuring accuracy and on-time submission.
• Serves as the organization’s Paychex system administrator: maintains user access and permissions, earnings and deduction codes, accrual and PTO rules, workflows, and standard/custom reports; tests and validates system and platform updates before they affect a live payroll. Acts as the primary liaison with Paychex (PEO) service, tax, and implementation teams; opens, tracks, and drives Paychex support cases to resolution and communicates status to Finance and HR.
• Reviews and reconciles timekeeping records against schedules, verifying hours, vacation, and leave balances before payroll processing. Calculates and pays meal and rest period premiums, reporting-time and split-shift pay, shift differentials, and other California-required payments identified through timekeeping review. Processes final wages within California deadlines — including all accrued, unused vacation or PTO.
• Verifies itemized wage statement content, paid sick leave accrual and balances, and required pay-related notices for California and San Francisco.
• Maintains current awareness of all new hires, terminations, transfers, promotions, pay changes, and leaves of absence, and enters or verifies each transaction in Paychex within required time frames, including tax withholding elections, direct deposit setup, and benefit-eligibility data. Partners with HR and hiring managers to confirm effective dates and pay rates before each payroll close. Keep all necessary parties informed.
• Calculates and processes benefit deductions, garnishments, and other with holdings in accordance with plan documents and legal orders.
• Manage and maintain record retention policies regarding employee reimbursements processed through payroll.
• Reconcile payroll registers,…