Benefits Payroll Manager

Agility Recruiting; San Francisco (CA); On-site; USD 103,500 - 126,500; Full time

Job summary

Agility Recruiting is seeking a Payroll and Benefits Manager to own full-cycle payroll in Paylocity for a nonprofit in San Francisco, handling tax reporting, deductions, and audit-ready recordkeeping to run payroll end-to-end with accuracy and compliance.

You will lead comprehensive benefits programs (medical, dental, vision, FSA/ commuter, life, disability), manage invoice reconciliation and premium audits, and collaborate with the broker on plan design and renewals.

Qualifications

• 4+ years of combined payroll and benefits management experience.
• Strong knowledge of CA labor law and SF ordinances.

Responsibilities

• Lead full-cycle, biweekly payroll in Paylocity for a nonprofit.
• Oversee benefits programs (medical, dental, vision, FSA/commuter, life, disability).
• Manage invoice reconciliation and premium auditing; partner with broker on plan design and renewals.
• Ensure audit-ready recordkeeping and end-to-end payroll compliance.

Skills

Payroll processing

Benefits administration

CA wage and hour law

Unionized environment

CBA terms knowledge

Education

SHRM Certification

Tools

Paylocity

Job description

Payroll and Benefits Manager Opportunity

A well established nonprofit is looking for a Payroll and Benefits Manager to own full cycle, biweekly payroll in Paylocity, from tax reporting and involuntary deductions to audit‑ready recordkeeping, giving someone the chance to run payroll end to end rather than just a piece of it.

This role comes with some real teeth: payroll experience within a unionized environment, applying CBA terms to compensation and overtime, plus deep CA labor‑law knowledge and hands‑on experience with San Francisco‑specific ordinances like HCSO. It’s a strong fit for someone who wants their compliance expertise to actually be used, not just checked off a list.

On the benefits side, this is a chance to lead, not just administer, full benefits programs across medical, dental, vision, FSA/commuter, life, and disability, with direct ownership of invoice reconciliation, premium auditing, and a seat at the table with the insurance broker on plan design and renewals.

Looking for 4+ years of combined payroll and benefits management experience; SHRM certification is a strong plus.

Compensation: $115,000 per year