Payroll Manager

About the role

Cold Spring Harbor Laboratory is seeking an experienced Payroll Manager to lead its payroll operations. This role offers the opportunity to oversee day-to-day payroll processing within Workday, manage complex tax reporting including Form 1042-S, and ensure a seamless payroll experience for more than 1,000 employees in a world-renowned research environment.

Responsibilities

• Payroll Operations: Process end-to-end, multi-cycle payroll in Workday, including calculating and reviewing earnings, deductions, and taxes, and performing detailed audits to ensure accuracy, timeliness, and regulatory compliance.
• Workday System Ownership: Act as the payroll subject matter expert within Workday, handling configuration, testing of updates and releases, troubleshooting, and collaborating with HRIS and IT on system enhancements.
• Team Leadership: Supervise, train, and develop payroll staff; define roles and responsibilities; and foster a culture of accuracy, service, and continuous improvement.
• Process Improvement: Identify and implement automation opportunities within Workday to minimize manual intervention and reduce errors.
• Cross-Functional Collaboration: Partner with Human Resources, Finance and Accounting, Office of Sponsored Programs, and other teams to maintain payroll data integrity and alignment across systems.
• Financial Analysis & Reporting: Analyze payroll-related financial data, prepare reports, and provide insights to support decision-making, budgeting, and cost control.
• Compliance: Ensure compliance with federal, state, and local payroll regulations and company policies; manage audits and internal controls; and stay current on evolving legislation.
• Foreign National Tax Withholding: Oversee foreign tax withholding requirements for foreign employees, instructors, and lecturers, ensuring accurate application of tax treaties and withholding rates.
• Year-End Tax Reporting: Lead year-end processing and filing of Forms W-2 and 1042-S, ensuring accuracy and timely delivery in accordance with IRS requirements.
• Payroll Costing: Manage payroll costing and labor distribution within Workday, ensuring accurate allocation of salaries, wages, and fringe benefits to grants, cost centers, and funding sources, and partner with Grants Management and Finance to resolve costing errors and support audit readiness.

Requirements

• Bachelor’s degree in Accounting, Finance, Human Resources, or a related field; or a related professional certification, such as a Certified Payroll Professional.
• Minimum 7 years of experience with automated payroll processing systems.
• Hands-on experience with Workday payroll, including configuration, testing, and troubleshooting.
• Working knowledge of Form 1042-S preparation, foreign national tax withholding, and applicable tax treaty rules.
• Strong understanding of federal, state, and local payroll tax regulations and multi-state payroll processing.
• Proven experience with year-end payroll processing, including W-2 and 1042-S reporting.
• Strong leadership and team management skills.
• Excellent communication, problem-solving, and organizational abilities.
• High level of accuracy and detail orientation, with strong data validation and audit habits.

Benefits

• Competitive pay
• Exceptional health benefits
• Retirement plans
• Paid time off
• Access to a Wellness Center
• Affordable and licensed on-site childcare center