The Payroll Manager leads end-to-end payroll operations for NEMS, ensuring accurate, timely pay for all employees while maintaining compliance with federal, state, and local payroll and tax regulations. This role supervises payroll staff, manages payroll systems and vendor relationships, delivers month end and year end payroll reconciliations and reports, and partners with HR and Finance on benefits, tax, and audit activities.
ESSENTIAL JOB FUNCTIONS:
- Oversees and executes full-cycle payroll for all employees, including gross-to-net calculations, deductions, garnishments, taxes and net payments
- Maintains and configures payroll system (Paycom); leads system implementations, upgrades, testing, and integrations with HRIS and general ledger
- Prepares, reconciles, and analyzes payroll journals and general ledger payroll accounts monthly; resolves discrepancies with Finance and HR.
- Ensures timely and accurate filing and payment of payroll taxes and related returns (federal, state, local) and oversees year-end processing (W-2s, 1095s as required).
- Administers payroll-related benefits deductions (health, retirement, flexible spending, commutes) and coordinates with Benefits/HR vendors.
- Manages wage garnishments, levies, and third-party wage attachments to ensure compliance and timely remittance.
- Serves as primary liaison for external payroll vendors, auditors, and government agencies during audits or inquiries.
- Develops, documents, and maintains payroll policies, procedures, and internal controls; recommends process improvements and automation to increase accuracy and efficiency
- Monitors payroll compliance with regulatory changes; researches and implements changes to maintain compliance with labor and payroll laws
- Provides clear payroll reporting and analytics to leadership (headcount, labor costs, overtime, payroll tax liabilities, trend analysis)
- Supports payroll portion of mergers/acquisitions, terminations, and employee offboarding when required
- Maintains confidentiality of payroll and compensation data and ensures secure handling of employee information
- Direct supervision of a department involving responsibility for results in terms of costs, methods and personnel. Responsible for carrying out supervisory/managerial responsibilities in accordance with the organization's policies and applicable laws. Responsibilities include interviewing and hiring of employees; planning, assigning, scheduling, and directing work; appraising performance; rewarding and disciplining employees; addressing complaints and resolving problems.
- Performs other job duties as required by manager/supervisor.
- Bachelor’s degree in Accounting, Finance, Human Resources, or related field
- Minimum 5 years of progressive payroll experience; at least 2 years in a supervisory or lead role
- Strong working knowledge of payroll laws, wage and hour regulations, payroll tax requirements, and best practices
- Hands-on experience with enterprise payroll/HCM systems and payroll tax filing processes
- Experience with Paycom Payroll is a plus
- Must have advanced spreadsheet skills, pivot tables, filtering and creating ad hoc reports
- Must have excellent organization skills, attention to details and ability to meet deadlines
- Ability to work both independently and effectively in a team environment
- Comprehensive knowledge of accounting & payroll processing in the healthcare or non-profit setting is a plus
- Certified Payroll Professional (CPP) or Fundamental Payroll Certifications (FPC) is preferred
LANGUAGE:
- Must be able to read, write and speak English fluently
- The ability to speak a second language is an asset
STATUS:
- This is a FLSA Exempt position.
- This is not an OSHA high-risk position.
- This is a Full Time position.
NEMS BENEFITS: Competitive benefits, including free medical, dental and vision insurance for employee, spouse and/or children; and company contribution to 401(k).
Skills Required
- Bachelor's degree in Accounting, Finance, Human Resources, or a related field
- At least 5 years of progressive payroll experience
- At least 2 years of supervisory or lead experience
- Strong knowledge of payroll laws, wage and hour regulations, payroll taxes, and payroll best practices
- Hands-on experience with enterprise payroll or HCM systems and payroll tax filing processes
- Advanced spreadsheet skills, including pivot tables, filtering, and ad hoc reporting
- Excellent organization, attention to detail, and ability to meet deadlines
- Ability to work independently and effectively in a team environment
- Fluent English reading, writing, and speaking skills
- Experience with Paycom Payroll
- Knowledge of accounting and payroll processing in a healthcare or nonprofit setting
- Certified Payroll Professional (CPP) or Fundamental Payroll Certification (FPC)
- Ability to speak a second language
What We Do
North East Medical Services (NEMS) is a non-profit community health center that provides affordable, comprehensive, and compassionate healthcare services to the San Francisco Bay Area. Targeting medically underserved and low-income populations, NEMS operates numerous clinics offering primary care, dental, and behavioral health services, delivering linguistically competent and culturally sensitive care in multiple languages to improve the overall well-being of the community.









