The Senior Manager, HRIS, Benefits & Compensation 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.

Key Responsibilities

HRIS Strategy, Governance, and System Administration

System Ownership{{:}} Serve as the primary administrator for the HRIS platform (currently ADP TotalSource) as well as the benefits (bSwift), compensation, performance review (Culture Amp), talent acquisition (Workable), learning and development platform (Veeva), and 401k platforms, overseeing configuration, integration between systems, workflows, and system settings.

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

Data Integrity & Auditing{{:}} Own the accuracy of all employee transactions and system communications. Perform regular HRIS systems audits, validations, and data cleanup to ensure "audit-ready" status in alignment with internal control documents.

Security & Access{{:}} Manage user permissions, security roles, and system protocols to maintain data privacy and compliance.

Optimization & Support{{:}} Troubleshoot complex system issues, coordinate with vendor support, and stay current on new features and best practices to optimize system functionality.

Benefits And Compensation

Benefits Oversight{{:}} Manage the full lifecycle of employee benefits programs, including open enrollment, vendor management, and ensuring seamless integration between the HRIS and external providers.

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.
Conduct audits and reporting requirements related to benefits programs
Maintain accurate plan documentation and required regulatory filings

Compensation Administration{{:}} Support the Head of People & Culture in the administration of compensation structures, including base pay, bonuses, and equity. Responsible for carrying out year-end merit cycle.

Market Benchmarking{{:}} Assist in conducting regular market salary surveys and benchmarking to ensure competitive and equitable pay scales.

System Alignment{{:}} Ensure all compensation and benefits data is accurately reflected in the HRIS for payroll processing and financial reporting.

Leave of Absence Administration{{:}} 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.

Employee Handbook Maintenance{{:}} Responsible for annual review and updates to employee handbook.

Reporting & Data Analytics

Insight Generation{{:}} Design, build, and maintain a library of standard and ad hoc reports for People & Culture, Finance, and Executive leadership
Advanced Analytics{{:}} Deliver custom analytics regarding employee data, turnover trends, and benefit/compensation utilization to drive data-informed decision-making

Compliance Reporting{{:}} Prepare and file required compliance reports (5500s, ACA reporting, non-discrimination testing).

Requirements

Experience{{:}} 10+ years of experience in HRIS management and benefits administration; prior experience in a "Manager" or "Lead" capacity preferred.

Technical Proficiency{{:}} Advanced expertise in ADP TotalSource (or similar Tier-1 HRIS like Workday or UKG) is required.

Analytical Skills{{:}} High proficiency in Microsoft Excel (VLOOKUPs, Pivot Tables, Advanced Formulas) and the ability to interpret complex datasets.

Education{{:}} Bachelor's degree in Human Resources, Business Administration, Information Technology, or a related field.

Compliance Knowledge{{:}} Strong understanding of ERISA, COBRA, HIPAA, FLSA, and FMLA regulations.

Preferred Qualifications

Certifications{{:}} SHRM-CP/SCP, PHR/SPHR, or Certified Professional in HRIS (CPHRIS).

Implementation Experience{{:}} Previous experience leading or assisting in a system implementation or migration.

Communication{{:}} Proven ability to translate technical system language into clear, actionable information for non-technical stakeholders.

Compensation

For candidates based in the SF Bay Area, the expected base salary range for this role is $170,000 - 205,000

For candidates based outside the SF Bay Area, the expected base salary range for this role is 150,000 - 180,000

The actual base pay offered will depend on factors such as experience, skills, and location. Employees in this role are also eligible to participate in our annual bonus and stock option program.

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.

Encoded is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Encoded is committed to the principle of equal employment opportunity for all employees and to providing employees with a work environment free of discrimination and harassment. All employment decisions at Encoded are based on business needs, job requirements and individual qualifications, without regard to race, religion or belief, color, national origin, gender, status as a protected veteran, status as an individual with a disability, or any other status protected by the laws or regulations in the location in which we operate. Encoded will not tolerate discrimination or harassment based on any of these characteristics. Encoded encourages applicants of all ages.

If you need assistance or an accommodation due to a disability, you may call us at +1 650-491-0272.

Encoded Therapeutics Inc. jobs

Senior Manager - HRIS, Benefits & Compensation

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