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Assistant Controller

Merlin Labs

Job Location:

Boston, MA - USA

Monthly Salary: Not provided by the employer

Posted: 17 June 2026 (30+ days ago)

Application Deadline: 24 October 2026

Vacancies: 1 Vacancy

Job Summary

About Merlin:

Merlin is a venture backed aerospace startup building a non-human pilot to enable both reduced crew and uncrewed flight. Backed by some of the worlds leading investors Merlin is scaling alongside our customers to begin leveraging autonomy today to solve some of aviations biggest challenges.

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.

Responsibilities:

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 companys 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 companys 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 companys 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 companys 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.

Qualifications:

Bachelors degree in Accounting Finance or a related field.
CPA license required (active and in good standing).
Minimum 7 years of progressive accounting experience with at least 3 years in a defense aerospace or government contracting environment.
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).

Nice to Have:

Masters degree in Accounting or Business Administration (MBA).
Experience at a Big 4 or national public accounting firm with a defense/government practice.
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.

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

Once youre here youll 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: emailprotected

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

Required Experience:

Junior IC

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