Director, Assistant Controller

Job Description

Job Description

About Merlin:

Merlin (NASDAQ: MRLN) is a publicly traded aerospace and defense company building a non-human pilot to deliver full-stack autonomy for any aircraft from takeoff to touchdown. The Merlin Pilot autonomy system powers a growing range of aircraft and mission profiles and has been proven through hundreds of autonomous flights from Merlin's global flight test facilities, including Kerikeri, New Zealand; Quonset Point, Rhode Island; and soon, Bedford, Massachusetts. Headquartered in Boston, Merlin is expanding its organization to accelerate the development and deployment of its autonomy platform, helping customers solve some of aviation's most pressing challenges, from pilot shortages to improving flight safety. Backed by some of the world's leading investors prior to its public listing, Merlin continues to advance the certification and commercialization of autonomous flight across commercial and defense aviation. 

About You: 

The Assistant Controller plays a critical role in the financial operations of Merlin, supporting the Corporate Controller in managing all aspects of accounting, financial reporting, internal controls, and compliance for a publicly traded government defense contractor. This position requires deep expertise in government contract accounting, SEC reporting obligations, and the unique regulatory environment governing defense industry finance. The Assistant Controller will lead a team of accounting professionals and serve as a key liaison between finance, program management, contracts administration, and external auditors.

Financial Reporting & SEC Compliance

• Assist in the preparation of quarterly (10-Q) and annual (10-K) reports filed with the Securities and Exchange Commission (SEC) in compliance with U.S. GAAP and PCAOB standards.

• Support Sarbanes-Oxley (SOX) Section 404 compliance, including documentation, testing, and remediation of internal controls over financial reporting (ICFR).

• Coordinate with external auditors (Big 4 or national firm) during quarterly reviews and annual audits.

• Prepare and review financial statements, footnotes, and MD&A disclosures for accuracy and completeness.

Government Contract Accounting

• Oversee cost accounting practices in compliance with the Federal Acquisition Regulation (FAR), Defense Federal Acquisition Regulation Supplement (DFARS), and Cost Accounting Standards (CAS).

• Manage the preparation and submission of government-required financial reports, including DCAA audits, incurred cost submissions (ICS), and forward pricing rate proposals (FPRPs).

• Monitor and maintain compliance with contract-specific accounting requirements, including time-and-materials (T&M), cost-plus-fixed-fee (CPFF), firm-fixed-price (FFP), and other contract types.

• Support the Earned Value Management (EVM) reporting process for applicable government programs.

General Accounting & Close Process

• Oversee the monthly, quarterly, and annual financial close process, ensuring accuracy and timeliness of all journal entries, account reconciliations, and financial statements.

• Manage indirect cost pools, allocation methodologies, and overhead rate calculations in compliance with CAS and FAR.

• Supervise revenue recognition under ASC 606, including over-time recognition methodology for long-term government contracts.

• Maintain and strengthen the company’s chart of accounts and general ledger integrity.

Internal Controls & Process Improvement

• Design, implement, and monitor effective internal control procedures in accordance with COSO framework and SOX requirements.

• Identify opportunities to streamline accounting processes and improve the efficiency and accuracy of financial operations.

• Develop and maintain accounting policies and procedures documentation.

Equity Administration

• Oversee the accounting and administration of the company’s equity compensation programs, including stock options, restricted stock units (RSUs), and the Employee Stock Purchase Plan (ESPP).

• Ensure accurate recording of stock-based compensation expense in accordance with ASC 718, including fair value determination, vesting schedules, and forfeiture rate assumptions.

• Coordinate with the company’s equity plan administrator and transfer agent to maintain accurate cap table records and equity award activity.

• Prepare equity-related financial statement disclosures and footnotes for SEC filings, including 10-K and 10-Q reports.

• Partner with Legal, HR, and Tax to administer Section 16 reporting obligations, Rule 10b5-1 trading plans, and insider trading policy compliance.

• Monitor and account for dilutive securities and ensure accurate earnings per share (EPS) calculations under ASC 260.

Payroll Oversight

• Oversee the company’s payroll function, ensuring accurate and timely processing of multi-state payroll for all employees, including salaried, hourly, and contract labor populations.

• Ensure compliance with federal, state, and local payroll tax regulations, including proper withholding, remittance, and year-end W-2 and 1099 reporting.

• Maintain payroll controls and procedures that satisfy SOX internal control requirements and DCAA labor charging standards.

• Coordinate with Human Resources on compensation changes, benefits deductions, leave accruals, and onboarding/offboarding processes to ensure payroll accuracy.

• Review and approve payroll journal entries, reconcile payroll liability accounts, and ensure proper allocation of labor costs to government contract cost pools and direct/indirect categories.

• Manage relationships with third-party payroll service providers and ensure system integrations with the ERP and time-tracking platforms are functioning accurately.

Team Leadership & Cross-Functional Collaboration

• Supervise, mentor, and develop a team of accounting professionals including Senior Accountants and Staff Accountants.

• Partner with Program Managers, Contracts Administration, Legal, and Finance to ensure accurate project-level financial reporting and forecasting.

• Support the CFO and Corporate Controller in special projects, M&A due diligence, and strategic financial initiatives.

• Bachelor’s degree in Accounting, Finance, or a related field.

• CPA license required (active and in good standing).

• Minimum 7 years of progressive accounting experience

• Demonstrated experience with FAR, DFARS, CAS, and DCAA audit processes.

• Strong working knowledge of U.S. GAAP, SEC reporting requirements, and SOX compliance.

• Experience with revenue recognition under ASC 606 for long-term contracts.

• Proficiency with ERP systems (Deltek Costpoint, SAP, or similar government contracting ERP strongly preferred).

• U.S. citizenship required (per government contract obligations).

• Master’s degree in Accounting or Business Administration (MBA).

• Experience at a Big 4 or national public accounting firm with a defense/government practice.

• Experience in a defense, aerospace, or government contracting environment.

• Familiarity with Earned Value Management (EVM) and EVMS compliance.

• Experience supporting IPO, secondary offerings, or public company transitions.

• Knowledge of AI/software development project cost accounting and R&D capitalization under ASC 350-40.

The compensation range provided is reflective of base salary only , and is a good-faith estimate based on a wide range of factors. The actual offer will be determined by a variety of factors including the candidate's qualifications, skills, experience, education, and training. Highly competitive equity grants are considered part of Merlin's total compensation package. Additionally, Merlin offers top-tier benefits for full-time employees.

This position is based on-site at Merlin HQ in Boston, MA.

Once you’re here, you’ll enjoy a variety of on-site perks designed to make your workday enjoyable and convenient. These include catered lunches featuring a rotating menu of delicious options, an assortment of snacks to keep you fueled throughout the day, and a selection of beverages, including coffee, tea, and other drinks, to keep you refreshed.

Our goal is to create an environment where you can thrive both professionally and personally.

Merlin Labs offers an innovative, entrepreneurial, and team-focused startup environment. We also offer a top-notch benefits package (health, dental, life, unlimited vacation, and 401k with match) and work/life integration. Being part of the Merlin team allows you to become part of a small team that supports professional development while working together to achieve our mission.

Merlin Labs is an equal opportunity employer and values diversity. We do not discriminate on the basis of race, religion, color, national origin, genetic information, sex (including pregnancy), gender, gender identity and expression, sexual orientation, age, marital status, military service or obligation or disability status, or any other characteristic protected by law. All job offers are contingent upon the candidate passing background and reference checks.

At this time, we are unable to provide visa sponsorship or consider candidates who require visa transfers. Applicants must be authorized to work in the United States without the need for visa sponsorship now or in the future. 

In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and to complete the required employment eligibility verification form upon hire.

If you require reasonable accommodation in completing an application, interviewing, completing any pre-employment testing, or otherwise participating in the employee selection process, please direct your inquiries to: View email address on ziprecruiter.com

Merlin Labs does not accept unsolicited resumes from any source other than directly from candidates.