Payroll Specialist w Paychex Flex experience in San Francisco, California at Wayward Medical Management Inc

POSITION SUMMARY
The Payroll Specialist coordinates with the TPA to ensure compliant, timely completion of payroll activities, in alignment with wage-and-hour law, tax withholding, and benefit deduction requirements across the practice’s 3 legal entities. This position maintains payroll records, resolves discrepancies, and supports payroll-related reporting for the organization. The role has limited independent decision-making authority and works under supervision, escalating classification, deduction, or leave questions to the Controller or Director of Finance. Errors in this role can directly affect employee pay accuracy, tax compliance, and the practice’s regulatory standing.
ESSENTIAL FUNCTIONS
• Ensures processing of bi-weekly payroll for all employees and providers, including hourly, salaried, and overtime calculations, ensuring accuracy and on-time submission in conjunction with the TPA.
• Reviews and reconciles timekeeping records against schedules, verifying hours, vacation, and leave balances before payroll processing.
• Processes payroll accurately across the organization’s multiple legal entities, ensuring correct entity-level tax IDs, general ledger coding, and cost allocation for each pay cycle.
• Calculates and processes benefit deductions, garnishments, and other withholdings in accordance with plan documents and legal orders.
• Reconciles payroll registers, tax filings, and general ledger entries; researches and resolves payroll discrepancies.
• Partners with the practice’s Paychex TPA relationship to ensure clean, on-time federal, state, and local payroll tax filings and reporting across all entities; monitors for filing errors or agency notices and resolves discrepancies directly with Paychex.
• Maintains accurate, confidential payroll records and ensures responses to employee pay, deduction, and W-2 inquiries, directly or through the TPA.
• Collects, prepares, and responds to requests for wage statements, pay data, and other reporting requests regarding pay history.
• Maintains regular and reliable attendance sufficient to meet the position’s operational, patient-service, and team obligations, with or without reasonable accommodation.
• Complies with applicable laws, regulations, accreditation requirements, privacy and security standards, and organizational policies relevant to the position.
The essential functions listed are intended to describe the fundamental duties of the position. A qualified individual must be able to perform these functions with or without reasonable accommodation. The organization will engage in a timely, good-faith interactive process when an accommodation is requested or the need for accommodation is known.
MARGINAL / OCCASIONAL FUNCTIONS
• Assists with processing expense reimbursements.
• Supports year-end payroll tasks, such as W-2 preparation and distribution.
MINIMUM REQUIRED QUALIFICATIONS
• Education: High school diploma or equivalent required; coursework in accounting, bookkeeping, or business administration preferred.
• Experience: Minimum two years of payroll processing experience, preferably in a medical or professional services setting.
• Licensure/Certification: None required to enter the role.
• Knowledge/Skills: Working knowledge of California and federal wage-and-hour law and payroll tax requirements; proficiency with spreadsheet applications; strong numerical accuracy, attention to detail, and organizational skills; ability to maintain confidentiality of sensitive pay and personnel information.
• Payroll Platform: Demonstrated, hands-on depth with Paychex Flex, including TPA-mediated tax filing and reporting workflows, sufficient to process payroll cleanly through the current TPA setup with minimal support.
• Other: Must be able to pass a background check as required for employment in a healthcare setting.
PREFERRED QUALIFICATIONS
• Fundamental Payroll Certification (FPC) or similar credential; experience with multi-state payroll; experience administering payroll across multiple legal entities within a single Paychex/TPA setup; interest in growing into Paychex configuration and payroll system strategy as the practice adds entities or locations.