Payroll and Benefits Specialist

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Looking for work that is both meaningful and challenging? At Missionwell, you can use your payroll expertise to support nonprofit organizations doing important work in their communities.

Missionwell provides HR, accounting, finance, payroll, and administrative support exclusively to nonprofits, including public charities, private and religious schools, and churches. When you join Missionwell, you become part of a mission-driven team helping organizations thrive so they can make a greater impact.

Position Summary

The Payroll and Benefits Specialist is responsible for the accurate, timely, and compliant processing of payroll and benefits administration for multiple nonprofit business partners. This full-time role focuses on payroll operations, benefits support, open enrollment coordination, deduction accuracy, reconciliation, compliance testing support, and related reporting. The Payroll and Benefits Specialist manages payroll from data collection through transmission, reconciliation, reporting, compliance review, and issue resolution, while also helping ensure benefit elections, deductions, invoices, and related records are accurate and aligned across payroll, HRIS, carrier, and broker systems.

The ideal candidate is a dependable payroll and benefits professional with excellent communication and time management skills who can manage multiple payroll calendars, support benefits administration deadlines, explain payroll and benefits matters clearly, and work independently in a fully remote environment. This position serves as a trusted payroll and benefits resource to business partners and collaborates with Missionwell team members, brokers, carriers, vendors, and client contacts to deliver accurate, responsive, and high-quality support.

Primary Responsibilities

• Process bi-weekly, semi-monthly, monthly, and off-cycle payrolls accurately and on time for multiple assigned business partners.
• Manage multiple payroll calendars, deadlines, and workflows to ensure all transactions are completed accurately and on time.
• Collect, review, and process timecards, payroll approvals, new hires, terminations, employee status changes, pay rate changes, bonuses, commissions, retroactive adjustments, reimbursements, and other payroll changes.
• Reconcile payroll registers, preview reports, deductions, taxes, accruals, and year-to-date balances before payroll transmission, and validate final payroll reports after processing.
• Process manual checks, payroll corrections, severance payments, and final wages in accordance with applicable federal, state, and local requirements.
• Apply appropriate tax treatment to wages, employer-paid benefits, fringe benefits, stipends, special payouts, and other compensation.
• Calculate and process wage garnishments and other authorized deductions in compliance with applicable requirements.
• Maintain accurate payroll and benefits data by entering, updating, reviewing, and reconciling employee and employer deductions, benefit changes, arrears, corrections, eligibility records, carrier invoices, enrollment records, and vendor reports.
• Administer time and attendance processes and coordinate accurate data flow between timekeeping, payroll, and HRIS systems.
• Coordinate and manage open enrollment activities, including employee communication support, benefit election tracking, system updates, deduction setup, payroll coordination, and post-enrollment review.
• Support broker, carrier, and vendor relationships by helping coordinate information requests, benefit changes, renewals, reporting needs, and issue resolution.
• Assist with benefits testing and compliance support, including gathering data, reviewing benefit-related payroll records, supporting nondiscrimination or eligibility testing, and preparing documentation as needed.
• Review payroll data for completeness, accuracy, and compliance; research discrepancies and resolve payroll issues promptly.
• Maintain accurate employee payroll records and supporting documentation in accordance with internal standards and record-retention requirements.
• Prepare accurate and timely year-end payroll reporting, including Forms W-2 and W-2c, as applicable.
• Research and assist with payroll tax notices, agency correspondence, and payroll-related compliance questions.
• Support payroll, benefits, and workers’ compensation audits by gathering data, preparing reports, organizing documentation, reconciling records, and responding to follow-up requests.
• Create and maintain payroll import files, reports, checklists, procedures, and process documentation.
• Generate recurring and ad hoc payroll, labor, benefits, and operational reports for business partners and internal stakeholders.
• Support payroll and benefits implementations, system conversions, testing, and process improvement projects as assigned.
• Serve as the primary payroll and benefits contact for assigned business partners, communicating clearly regarding deadlines, approvals, corrections, documentation, benefit deductions, open enrollment tasks, payroll requirements, and related issue resolution.
• Explain payroll calculations, earnings, deductions, tax treatment, benefit deductions, enrollment impacts, and compliance requirements in clear, professional, and easy-to-understand language.
• Collaborate with HR, Benefits, Accounting, Operations, brokers, carriers, payroll vendors, and software providers to ensure accurate payroll and benefits administration and timely issue resolution.
• Maintain strict confidentiality and use sound judgment when handling payroll, employee, and organizational information.

California Payroll Compliance Responsibilities

Maintain current working knowledge of California wage, labor, employment, and payroll compliance requirements and apply that knowledge to assigned payrolls, including:

• Regular and daily overtime calculations
• Meal and rest period premium pay
• Minimum wage and applicable local wage ordinances
• Final pay timing and calculation requirements
• Paid sick leave requirements and payroll treatment
• Wage statement requirements
• Expense reimbursement and taxable benefit considerations
• Employee classification and timekeeping considerations
• Payroll recordkeeping and retention requirements
• Benefit deduction accuracy, taxable benefit treatment, and payroll-related benefits compliance support

Monitor payroll and benefits practices for potential compliance concerns, research questions when needed, elevate complex matters appropriately, and communicate relevant changes to internal team members and business partners.

Requirements

Qualifications

• Associate degree in Accounting, Business Administration, Human Resources, Payroll Administration, or a related field required; equivalent directly related experience may be considered.
• At least 4 years of payroll processing experience required, including at least 2 years of California payroll processing experience.
• Experience managing payroll for multiple entities, clients, or payroll groups simultaneously.
• Strong working knowledge of California wage-and-hour, payroll, final pay, wage statement, sick leave, deduction, and recordkeeping requirements.
• Experience supporting benefits administration functions such as open enrollment, deduction updates, reconciliations, broker or carrier coordination, and compliance-related testing preferred.
• Strong knowledge of federal, state, and local payroll tax regulations, garnishments, taxable wages, benefit deductions, taxable benefits, and payroll processing procedures.
• Excellent written and verbal communication skills, including the ability to explain payroll and benefits information clearly and professionally.
• Excellent time management, organization, prioritization, and deadline management skills.
• Exceptional attention to detail and commitment to accuracy.
• Strong analytical, reconciliation, decision-making, and problem-solving skills.
• Ability to work independently, manage competing priorities, adapt to change, and know when to seek support or elevate an issue.
• Demonstrated dependability, responsiveness, discretion, and commitment to exceptional client service.
• Proficiency with Microsoft 365 and the ability to learn new systems quickly.
• Experience with payroll, HRIS, and benefits administration platforms such as ADP, BambooHR, Gusto, isolved, Paychex, Paylocity, Rippling, carrier portals, broker platforms, or similar systems preferred.
• Multi-state payroll experience is strongly preferred.
• Experience supporting nonprofit or religious organizations is a plus.

All Missionwell Staff Are Required To

• Maintain accurate project action items and status updates in Missionwell’s project management tools and complete timekeeping accurately and on time.
• Stay informed of organizational announcements, activities, and changes through Missionwell communication tools and participation in staff meetings.
• Maintain strict confidentiality in all aspects of the job.
• Attend and participate in staff and team meetings as requested.
• Perform other payroll- and benefits-related duties and responsibilities as assigned.

Schedule

This is a full-time position. The employee must maintain a consistent work schedule aligned with Pacific Time business hours and be available during payroll processing deadlines and other time-sensitive payroll periods.

Work Location and Technology Requirements

• This is a fully remote, California-based position. Occasional travel may be required.
• A dedicated, distraction-free workspace that provides privacy for confidential conversations and payroll work.
• Reliable high-speed internet access and the ability to work effectively and securely in a remote environment.

Physical Requirements

• Ability to read, write, communicate effectively, and perform payroll-related mathematical calculations.
• Extended periods of sitting and working at a computer.
• Repetitive hand, arm, and finger movement when using a keyboard and mouse.
• Ability to lift and carry up to 25 pounds occasionally.