Payroll Manager

Cold Spring Harbor Laboratory; Plainview (NY); On-site; USD 100,000 - 115,000; Full time

Benefits offered by this job

Health benefits

Retirement plans

Paid time off

Wellness programs

Job summary

Cold Spring Harbor Laboratory is seeking an experienced Payroll Manager to lead our payroll operations in a cutting-edge research environment. This role manages end-to-end payroll processing in Workday for 1,000+ employees, handling complex tax reporting including 1042-S and W-2, and ensuring compliance and accuracy across all cycles.

The successful candidate will lead a payroll team, collaborate with HR and Finance, and drive process improvements to reduce errors and increase efficiency while

Qualifications

• Hands-on Workday payroll configuration, testing, and troubleshooting.
• Experience with Form 1042-S preparation and withholding rules.
• Strong knowledge of federal, state, and local payroll tax regulations.

Responsibilities

• Process end-to-end, multi-cycle payroll in Workday.
• Lead payroll staff and develop a high-performing team.
• Ensure accuracy, timeliness, and regulatory compliance of all payrolls.
• Oversee year-end tax reporting: W-2 and 1042-S.
• Coordinate with HR, Finance, and Grants to optimize cost distribution.
• Identify and implement payroll automation opportunities.
• Maintain internal controls and audit readiness across payroll.

Skills

Workday payroll

1042-S reporting

W-2 reporting

Foreign tax withholding

Team leadership

Tax compliance

Education

Bachelor's degree

Tools

Workday

Job description

Position Description

Are you passionate about payroll excellence and driving accuracy, compliance, and efficiency in a cutting-edge research environment? Cold Spring Harbor Laboratory is seeking an experienced Payroll Manager to lead our payroll operations. This is an exciting 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 our 1,000+ employees.

Position Responsibilities

As Payroll Manager, you will be a key member of the Finance team, contributing to the Laboratory's success in the following ways:

1. Payroll Operations: Hands-on processing of end-to-end, multi-cycle payroll within Workday, including calculating and reviewing earnings, deductions, and taxes, and performing detailed audits of each payroll run to ensure accuracy, timeliness, and compliance with all applicable regulations.
2. Workday System Ownership: Serve as the payroll subject matter expert within Workday, including configuration, testing of updates and releases, troubleshooting, and partnering with HRIS and IT on system enhancements.
3. Team Leadership: Supervise, train, and develop payroll staff; establish clear roles and responsibilities and foster a culture of accuracy, service, and continuous improvement.
4. Process Improvement: Identify and implement opportunities for payroll process automation and efficiency within Workday, minimizing manual intervention and reducing errors.
5. Cross-Functional Collaboration: Develop strong partnerships with Human Resources, Finance and Accounting, Office of Sponsored Programs, and other Laboratory teams to ensure payroll data integrity and alignment across systems.
6. Financial Analysis & Reporting: Analyze payroll-related financial data, prepare reports, and provide insights to support decision-making, budgeting, and cost control.
7. Compliance: Ensure compliance with federal, state, and local payroll regulations and company policies; manage payroll audits and internal controls, and stay current on evolving payroll legislation.
8. Foreign National Tax Withholding: Oversee foreign tax withholding requirements for foreign employees, instructors, and lecturers, ensuring accurate application of tax treaties and withholding rates.
9. 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.
10. Payroll Costing: Manage payroll costing and labor distribution within Workday, ensuring salaries, wages, and fringe benefits are accurately allocated to the correct grants, cost centers, and funding sources, and partner with Grants Management and Finance to resolve costing errors and support audit readiness.

Position Requirements

Education: Bachelor's degree in Accounting, Finance, Human Resources, or related field; or a related professional certification, such as a Certified Payroll Professional.

Experience: Minimum 7 years' experience with automated payroll processing systems.

Knowledge/Skills Required:

• Demonstrated 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.

Supplemental Information

Environment

Cold Spring Harbor Laboratory is a world-renowned biomedical research institution in New York. It has shaped contemporary biomedical research and is the home of eight Nobel Prize laureates. Cold Spring Harbor Laboratory provides a highly dynamic and interactive research environment and also a unique opportunity of timely exposure to advances in various biomedical research fields and of interaction with a broad range of researchers from all over the world through its renowned Meetings and Courses program. We believe that science is for everyone. We have had researchers with a variety of backgrounds and believe in the importance of diversity, equity, and inclusion.

Compensation and Benefits

Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our CSHL Benefits sites to learn more. The salary range for this role is $100,000 - $115,000. The salary range and/or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a base salary and/or rate, several factors may be considered as applicable (e.g., years of relevant experience, education, credentials, and internal equity).

CSHL is an EO Employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or protected veteran status. VEVRAA Federal Contractor