Payroll Administrator

Samaritan House of San Mateo County; San Mateo (CA); On-site; USD 70,000 - 90,000; Full time

Job summary

Samaritan House of San Mateo County seeks a Payroll Administrator under the Controller to manage bi-weekly payroll, timekeeping, and related HRIS systems, ensuring accuracy and regulatory compliance.

The role collaborates with HR and Finance, supports grant-funded payroll allocations, and maintains detailed labor and benefits records while meeting deadlines.

Candidates should have 3–5 years of experience; associate degree; CPP/FPC preferred; strong Excel skills.

Qualifications

• 3-5 years of payroll administration experience.
• Experience with processing multi-department payrolls.
• Knowledge of California payroll regulations and compliance.
• Experience with nonprofit/grant-funded payroll preferred.
• Strong Excel and payroll reporting skills.
• Experience with Paylocity or similar HRIS systems.
• Ability to work independently while collaborating with teams.

Responsibilities

• Process bi-weekly payroll accurately and timely.
• Ensure payroll compliance with policies and regulations.
• Review timesheets and payroll entries for accuracy.
• Process payroll changes including hires, terminations, and adjustments.
• Coordinate with HR, Benefits, and Finance on payroll matters.
• Prepare payroll reports and journal entries for ledger.

Skills

Payroll administration

Multi-department payroll

Paylocity

Nonprofit payroll

CA payroll compliance

Advanced Excel

HRIS systems

Analytical skills

Education

Associate's Degree in related field

CPP/FPC preferred

Tools

Paylocity

HRIS platforms

Excel

Job description

Under the general supervision of the Controller, the Payroll Administrator is responsible for the accurate and timely processing of payroll, payroll accounting, employee benefit deductions, electronic timekeeping and scheduling administration, labor allocation reporting, payroll compliance, and payroll-related financial reporting. The Payroll Administrator serves as the primary administrator of the Agency's payroll, timekeeping, scheduling, and payroll-related HRIS systems and works closely with Human Resources, Finance, and departmental leadership to ensure accurate payroll processing, labor allocations, regulatory compliance, and employee support. This position plays a critical role in maintaining the integrity of payroll and workforce data while supporting the Agency's operational and financial objectives.

JOB QUALIFICATION

Please note our preferred and in some cases required qualifications for this position:

EDUCATION:

• Associate's Degree in Accounting, Business Administration, Human Resources, Finance, or a related field preferred.
• Certified Payroll Professional (CPP) or Fundamental Payroll Certification (FPC) preferred.

EXPERIENCE:

• 3-5 years of payroll administration experience.
• Experience in processing multi-department payrolls and maintaining employee payroll records.
• Experience with Paylocity or similar payroll and HRIS systems preferred.
• Experience working with nonprofit organizations and grant-funded payroll allocations preferred.

KNOWLEDGE, SKILLS, AND ABILITIES:

• Thorough knowledge of payroll laws, wage and hour regulations, payroll tax reporting, and benefit deductions.
• Strong understanding of California payroll regulations and compliance requirements.
• Advanced Microsoft Excel skills and proficiency with payroll reporting tools.
• Demonstrated experience with payroll systems, HRIS platforms, and financial applications.
• Ability to work independently while maintaining strong collaborative relationships across departments.
• Strong attention to detail, organizational skills and ability to multitask/prioritize in a fast-paced work environment Commitment to excellence and high standards.
• Self-motivated; capable of developing analysis from ambiguous information with minimal or no supervision.
• Strong organizational, problem-solving, and analytical skills; proven ability to multi-task, manage workflow and meet deadlines.

ESSENTIAL FUNCTIONS OF THE JOB

Payroll Administration

1.Process bi-weekly payroll accurately and timely through the Agency's payroll system.

2.Ensure payroll is processed in compliance with Agency policies regarding timekeeping, attendance, overtime, meal periods, and leave administration.

3.Review employee timesheets, pay adjustments, leave balances, and payroll entries for completeness and accuracy.

4.Process payroll-related employee changes including new hires, terminations, salary adjustments, benefit deductions, status changes, and other compensation-related updates.

5.Follow up with supervisors and employees regarding missing, inconsistent, or inaccurate timekeeping information.

6.Maintain payroll schedules and ensure all payroll deadlines are met.

7.Prepare payroll import files and validate payroll data prior to processing.

8.Review payroll registers and reconciliation reports before payroll transmission.

9.Process off-cycle payrolls, adjustments, and special payments as needed.

10.Serve as primary liaison with Paylocity and other payroll vendors regarding system administration and payroll issues.

Electronic Timekeeping and Scheduling Administration

11.Serve as primary administrator for the Agency's electronic timekeeping and scheduling systems.

12.Monitor, audit, and resolve timekeeping exceptions, missed punches, schedule discrepancies, overtime, leave balances, and other payroll-related issues to ensure accuracy and compliance.

13.Work closely with managers and supervisors to ensure employee schedules and time records are maintained in accordance with Agency policies and labor regulations.

14.Provide training and support to employees and managers regarding timekeeping and scheduling system functionality, policies, and procedures.

15.Maintain employee scheduling configurations, pay codes, departmental assignments, labor distribution structures, and organizational hierarchies within the timekeeping and scheduling systems.

16.Generate and distribute timekeeping, attendance, overtime, and scheduling reports for management review.

17.Ensure timekeeping and scheduling systems are properly integrated with payroll and HRIS systems to support accurate payroll processing.

18.Maintain employee leave balances, including PTO, personal leave, and other applicable leave programs, and ensure balances are accurately reflected within payroll and timekeeping systems.

19.Identify opportunities to improve timekeeping, scheduling, and payroll workflows through process improvements, automation, and system enhancements.

Labor Allocation and Grant Funding Support

20.Generate and review labor distribution reports for management and grant reporting purposes.

21.Coordinate payroll allocations, labor distributions, and funding reallocations across programs, departments, grants, and funding sources in collaboration with Finance and program leadership.

Assist with payroll-related grant reporting, funding reconciliations, and labor allocation reviews to support compliance with grant and contract requirements.

Payroll Accounting, Reconciliations & Compliance

22.Prepare and record payroll-related journal entries in the general ledger, ensuring payroll expenses, taxes, benefits, and liabilities are accurately recorded and reconciled.

23.Prepare monthly benefits-related journal entries, including medical, dental, vision, retirement, life insurance, COBRA, and other employee benefit allocations.

24.Prepare and maintain payroll accrual, paid time off liability, and other employee compensation schedules, including related calculations and journal entries.

25.Coordinate with Human Resources, benefits providers, and Finance staff to ensure accurate employee deductions and employer benefit contributions.

26.Assist with cash forecasting by providing payroll and benefit expenditure projections.

27.Assist with month-end and year-end closing processes related to payroll and employee benefits.

28.Support annual audits by preparing payroll and benefits schedules and responding to auditor requests.

29.Ensure payroll expenses, taxes, and benefit costs are accurately allocated to departments, programs, grants, and funding sources.

30.Prepare and distribute payroll expenditure, labor allocation, and workforce cost reports for management and departmental review.

31.Reconcile payroll-related accounts, including payroll liabilities, accrued payroll, payroll taxes, benefit deductions, COBRA activity, garnishments, and other employee deductions; investigate variances and resolve discrepancies to ensure accurate financial reporting and compliance.

32.Assist with year-end payroll processes, including W-2 preparation, payroll audits, and regulatory reporting.

33.Maintain compliance with federal, state, and local payroll regulations.

34.Monitor payroll tax filings and payments processed by payroll vendors and ensure timely resolution of any discrepancies or notices.

35.Respond to payroll tax inquiries, audits, and agency correspondence as needed.

36.Prepare payroll reports and supporting documentation for audits, grant reviews, and management requests.

37.Maintain payroll procedures and documentation to support strong internal controls.

Benefit Administration and Reconciliation

38.Coordinate payroll-related benefit deductions and employer contributions for medical, dental, vision, life insurance, retirement plans, flexible spending accounts, and other employee benefit programs.

39.Reconcile benefit invoices and employee deductions monthly.

40.Work collaboratively with Human Resources and benefit providers to ensure accurate enrollment, deductions, terminations, and changes.

41.Assist employees with payroll-related benefit inquiries and resolution of deduction discrepancies.

42.Maintain benefit-related records and support documentation for audit and compliance purposes.

43.Support annual open enrollment and implementation of benefit plan changes as needed.

HRIS and System Administration

44.Maintain employee payroll records, payroll configurations, earnings codes, deduction codes, tax settings, and organizational structures within Paylocity and related systems.

45.Serve as system administrator for payroll, timekeeping, scheduling, and related HRIS applications.

46.Assist with payroll system enhancements, upgrades, testing, troubleshooting, and process improvements.

47.Support integration between payroll, timekeeping, scheduling, benefits, HRIS, and financial systems.

48.Develop and maintain payroll reports, dashboards, key performance indicators, and data analytics to support management decision-making.

49.Ensure data integrity, security, and confidentiality of employee payroll and personnel information.

50.Identify opportunities to improve payroll efficiency, accuracy, internal controls, and automation through system enhancements and process improvements.

51.Maintain payroll procedures, reference materials, and system documentation.

Other Duties and Responsibilities

55.Attend any assigned training or meetings internal or external- represent Samaritan House positively and professionally.

56.Provide payroll support and customer service to employees, supervisors, and department leaders.

57.Support Controller with other duties within the Finance and Data Departments as assigned.