Senior Manager HRIS, Benefits & Compliance

Encoded Therapeutics•South San Francisco, CA

5d•$150,000 - $205,000•Remote

About The Position

The Senior Manager, HRIS, Benefits & Compliance is responsible for leading the strategy, administration, and continuous improvement of the company’s Human Resources Information Systems and employee benefits programs. This role serves as the primary owner of HR systems infrastructure and benefits operations, ensuring data integrity, system optimization, regulatory compliance, and an exceptional employee experience. As the organization continues to scale, this role will partner closely with People & Culture leadership, Finance, Payroll, IT, and external vendors to ensure HR systems and benefits programs support a growing and geographically distributed workforce. This position combines strategic planning with hands-on operational ownership and is expected to drive process improvements, system enhancements, and data insights that support organizational growth. This role reports to the Head of People & Culture. Open to candidates based in California or US remote.

Requirements

Bachelor’s degree in Human Resources, Business Administration, Information Systems, or related field.
10+ years of progressive experience in HRIS administration and benefits management, including experience in high-growth or scaling organizations.
Strong experience administering modern HRIS platforms (e.g., ADP, Workday, UKG, Rippling, or similar).
Demonstrated experience managing vendor relationships including benefits brokers and third-party administrators.
Strong knowledge of employee benefits regulations and compliance requirements.
Experience supporting multi-state employee populations, with strong knowledge of California employment and benefits regulations preferred.
Advanced analytical and problem-solving skills with the ability to translate HR data into actionable insights.
Strong communication and cross-functional collaboration skills.

Nice To Haves

HRIS, benefits, or HR certification such as CEBS, CBP, SHRM-CP/SHRM-SCP, or SPHR.
Experience supporting HRIS implementations, system migrations, or major upgrades.
Experience supporting biotechnology, life sciences, or technology organizations strongly preferred, but not required.
Experience working in companies with fewer than 500 employees or in rapid growth environments.

Responsibilities

Own the overall administration, optimization, and governance of the company’s HRIS platform, including employee lifecycle transactions, workflows, reporting, and system configuration.
In partnership with IT, develop and execute an HRIS roadmap that supports organizational scaling, evolving business needs, and future technology integrations.
Serve as the primary system administrator responsible for maintaining system functionality, troubleshooting issues, managing upgrades, and coordinating system changes.
Lead evaluation and implementation of new HR technologies, integrations, and automation opportunities that improve HR operations and employee experience.
Ensure the accuracy, integrity, and security of employee data across HR systems.
Partner with IT, Payroll, and Finance to maintain integrations between HRIS, payroll, equity administration, and other enterprise systems.
Oversee the design, administration, and communication of employee benefits programs including medical, dental, vision, life, disability, wellness, retirement plans, and leave programs.
Partner with leadership and external brokers to evaluate benefits strategy and ensure competitive offerings aligned with biotech industry benchmarks in the San Francisco Bay Area.
Manage annual open enrollment planning, implementation, and employee communications.
Act as the primary point of contact for benefits vendors, brokers, and third-party administrators.
Provide guidance to employees regarding benefit programs, eligibility, and claims escalation when necessary.
Ensure compliance with all applicable federal, state, and local regulations related to benefits administration and HR data management including ERISA, ACA, HIPAA, COBRA, and state leave programs.
Maintain compliance with California-specific employment and benefits regulations including leave programs, pay transparency requirements, and reporting obligations.
Oversee administration of employee leave programs including FMLA, CFRA, Pregnancy Disability Leave (PDL), California Paid Family Leave (PFL), ADA accommodations, and workers’ compensation coordination, partnering with third-party administrators and ensuring compliance with California and federal regulations while supporting employees and managers throughout the leave lifecycle.
Support audits and reporting requirements related to HR systems and benefits programs.
Maintain accurate plan documentation and required regulatory filings.
Continuously evaluate HR systems and benefits processes to identify opportunities for automation, efficiency, and improved employee experience.
Develop and maintain system documentation, standard operating procedures, and training resources.
Provide training and guidance to HR team members and managers on HRIS functionality and benefits processes.

Benefits

Comprehensive benefits package, including competitive employer premium contributions
Meaningful stock option grants
PTO, sick time, and holiday pay
Generous Parental Leave program
Pre-tax medical and dependent care programs
STD, LTD, Life and AD&D
Professional development opportunities
Team-building events
Fully stocked kitchen
Fitness center at our SF office
Employees (and their families) may obtain medical, dental, vision and basic life insurance benefits through the company and enroll in our company's 401k plan. Employees will also accrue vacation time off and paid sick time off and may become eligible for paid parental leave. Employees will also enjoy designated paid holidays throughout the calendar year.