Associate Director, Payroll and Equity

Amylyx has an audacious mission to usher in a new era for treating diseases with high unmet needs. Where others see challenges, we see opportunities that we pursue with urgency, rigorous science, and unwavering commitment to the communities we serve. We are a clinical-stage company currently focused on post-bariatric hypoglycemia (PBH), Wolfram syndrome, and amyotrophic lateral sclerosis (ALS).

Our mission is powered by our people. Our core values – be audacious, be curious, be authentic, be engaged, and be accountable – creating a culture of caring. Amylyx has assembled an experienced team ready to take action because the communities we serve have no time to wait. If you share our passion and are determined to tackle some of medicine’s toughest problems, we encourage you to read the opportunity below and apply.

The Opportunity

Amylyx is seeking a highly motivated professional with extensive payroll and equity administration experience. This individual will play a crucial role in leading and optimizing our payroll processes and equity programs, ensuring compliance with federal and state regulations, and providing exceptional service to our employees. The ideal candidate will have a strong background in payroll and equity administration, excellent analytical and problem-solving skills, and the ability to thrive in a fast-paced and dynamic environment.

We anticipate hiring the Associate Director, Payroll and Equity in September 2026

Responsibilities

Payroll:

• Own the day-to-day processing of U.S. multi-state payroll using ADP, including garnishments, benefits and taxes to multi-site employees consistent with federal and state wage and hour laws.
• Partner with Human Resources to ensure employee transactions, including hires, terminations, promotions, transfers, and leaves of absence, are processed accurately and timely.
• Perform monthly payroll reconciliations, payroll journal entries, bonus accruals and resolve any payroll discrepancies in a timely manner.
• Own and maintain payroll controls and SOX-compliant processes, ensuring adherence to internal policies, regulatory requirements, and audit standards.
• Review and maintain the documentation of payroll reports, including semi-monthly, monthly, quarterly and year-end payroll reports (gross payroll, hours worked, accruals, tax deductions, benefit deductions, etc.).
• Manage and proactively address payroll-related inquiries from employees, HR and other functional teams; communicate with external stakeholders, such as federal and state tax authorities and Amylyx partners and vendors.
• Partner with ADP and other service providers to ensure accurate year-end processing and W-2 reporting; support workers' compensation, 401(k), payroll tax, and other payroll-related audits and compliance activities.
• Coordinate with third-party international payroll providers and internal stakeholders to support payroll activities and ensure accurate processing of payroll and equity-related transactions for international employees.
• Support the design, implementation, and continuous improvement of payroll and equity programs, processes, and controls.

Equity Compensation:

• Own the day-to-day administration of the company’s equity programs, including processing new stock awards, cancellations and exercises, and calculation of tax withholdings.
• Administer data in the equity trading platform (Shareworks) and transfer agent (Computershare), ensuring accuracy of participant information.
• Partner with Accounting, Legal, SEC Reporting, and Human Resources to support public company reporting and compliance requirements, including Forms 10-Q, 10-K, Proxy Statements, and Section 16 reporting.
• Reconcile equity activity and maintain accurate records of shares outstanding, share reserves, and participant balances.
• Maintain and enhance SOX-compliant controls, processes, and documentation related to equity administration.
• Serve as a trusted resource for employee and executive equity inquiries, education, and communications.
• Collaborate with the HR and Legal teams on equity-related topics.
• Assist with the development and delivery of employee trainings and communications.

Required Qualifications

• Bachelor's degree in Accounting, Finance, Business Administration, Human Resources, or a related field preferred; equivalent combination of education, professional certifications, and relevant experience will be considered.
• 8+ years of multi-state payroll experience, including hands-on administration of ADP Workforce Now or a similar enterprise payroll platform.
• 3+ years of equity administration experience supporting stock option and RSU programs in a public company environment.
• Experience supporting high-growth publicly traded companies, including quarterly and annual reporting requirements.
• Strong knowledge of federal, state, and local payroll tax regulations, including taxation related to equity compensation.
• Thorough understanding of payroll internal controls, reconciliations, and audit requirements.
• Advanced proficiency in Microsoft Excel, including Pivot Tables, XLOOKUP/VLOOKUP, data analysis, reconciliations, and reporting; strong working knowledge of Microsoft Office applications, including Word, PowerPoint, and Outlook.
• Excellent analytical, organizational, communication, and problem-solving skills, with strong attention to detail.
• Demonstrated ability to handle highly confidential information with discretion and maintain the highest professional and ethical standards in a fast-paced, cross-functional environment.

Preferred Requirements

• Certified Payroll Professional (CPP) and/or Certified Equity Professional (CEP) designation.
• Experience with Shareworks, Computershare, and NetSuite.
• Experience in the biotechnology, pharmaceutical, or life sciences industry.

Work Location and Conditions

• At Amylyx, we proudly support remote work opportunities within the United States. However, due to business considerations related to health insurance coverage and state tax regulations, we are unable to hire employees who reside and/or work in certain states. Currently, we are not considering applicants from Alaska, Arizona, Hawaii, Michigan and Tennessee.
• You will be expected to travel to our corporate location in Cambridge, MA several times a year and attend other company-related events as necessary and requested.
• You must have access to work in setting which enables meeting all requirements of the role (including privacy, reliable internet access, phone, ability to video conference, etc.) at your remote location.

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Amylyx Pharmaceuticals is an Equal Opportunity Employer that does not discriminate on the basis of actual or perceived race, color, creed, religion, national origin, ancestry, citizenship status, age, sex or gender (including pregnancy, childbirth, pregnancy-related conditions, and lactation), gender identity or expression (including transgender status), sexual orientation, marital status, military service and veteran status, physical or mental disability, genetic information, or any other characteristic protected by applicable federal, state, or local laws and ordinances. Amylyx’s management team is dedicated to this policy with respect to recruitment, hiring, placement, promotion, transfer, training, compensation, benefits, employee activities, access to facilities and programs, and general treatment during employment. Accommodations are available for candidates who require them in our selection process. If you need an accommodation, please let your Amylyx Talent Acquisition contact know.

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.