Corporate Accounting Manager

Warmada; San Francisco (CA); Hybrid; USD 180,000 - 240,000; Full time

Job summary

Benchling is seeking a Corporate Accounting Manager to own employee-compensation accounting, including payroll, commissions, bonuses, stock-based compensation, and benefits. Lead a team, ensure accurate close, strong controls, and scalable processes as the company grows.

The ideal candidate has hands-on experience with payroll, commissions and bonuses, SBC accounting at a high-growth SaaS company, strong US GAAP knowledge, and a passion for automation and AI-enabled workflows.

Qualifications

• 5+ years of related work experience. Big 4 or large regional public accounting firm experience is required, and at least 1 year of hands-on people management.
• Hands-on experience with payroll, commissions and bonuses, and stock-based compensation accounting under US GAAP.

Responsibilities

• Own payroll accounting and the payroll close process end to end in partnership with Payroll and HR, driving operational efficiencies.
• Review commission, bonus, sign-on, and retention accounting, including accruals and rollforwards; apply ASC 340-40 where applicable.
• Own stock-based compensation and equity accounting under ASC 718; review SBC entries and equity rollforwards, and draft equity footnote disclosures and supporting memos.
• Review benefits and other employee-related accounting, including worker’s compensation, health benefits, leaves, PTO, and 401(k) liabilities.
• Own the 409A valuation process and international pension coordination.
• Lead equity administration and compensation-system projects, such as the ASC 340 waterfall system adoption.
• Design, document, and maintain internal controls over payroll, bonus, SBC, and benefits in accordance with Sarbanes-Oxley.
• Manage internal and external inquiries and prepare audit support for owned areas to successfully execute quarterly and annual financial statement audits.

Skills

Payroll accounting

US GAAP knowledge

People management

Excel proficiency

Cross-functional collaboration

Analytical mindset

Communication

Confidential data handling

Automation mindset

Education

Bachelor's degree in Accounting or Finance

Tools

NetSuite

Carta

FloQast

Job description

We are rebuilding biotech for the AI era.

When a breakthrough is delayed, the world waits. Getting a molecule from discovery to patients, or a crop from lab to field, involves thousands of slow, manual, disconnected steps. AI has the potential to change this, compressing decades of R&D work into years. But that only happens when clean, structured scientific data and AI are built into how science gets done.

Benchling is the AI platform for biotech R&D. Scientists use Benchling to design experiments, capture structured data, and run AI agents and models directly in their workflows. Over 200,000 scientists around the world trust Benchling to power their most important work, from academic labs to Sanofi, Moderna, and more than half of the world's top 50 biopharma.

We’re building an AI scientist for our customers. We can’t do that if we haven’t built the muscle ourselves. AI fluency is the foundation we build on; it's core to how we work, and we're committed to helping every new hire integrate it into their day-to-day. As part of our interview process, you'll complete a brief AI-focused exercise or discussion so we can understand how you think about and use AI to drive impact in your role. Feel free to reference any tools, platforms, or workflows you use today.

ROLE OVERVIEW

We are looking for a Corporate Accounting Manager to take full ownership of employee-compensation accounting at Benchling, including payroll, commissions and bonuses, stock-based compensation and equity, and employee benefits. This leader will be accountable end to end for these areas: an accurate and timely close, strong controls and documentation, and the operational improvements that make these processes scalable as the Company grows.

The Manager will lead and develop the team members who prepare payroll and compensation entries, review their work, and partner closely with Payroll, HR, Legal, Strategic Finance, and external auditors. We expect this person to act as the owner of the area, escalating by exception rather than by default.

An ideal candidate has hands-on experience in payroll, commission and bonus, and stock-based compensation accounting at a high-growth SaaS company, a strong command of US GAAP, and a passion for improving how work gets done, including through automation and AI tools.

RESPONSIBILITIES

Employee Compensation Accounting

• - Own payroll accounting and the payroll close process end to end in partnership with Payroll and HR, and drive operational efficiencies in the related processes.
• - Review commission, bonus, sign-on, and retention accounting, including accruals, prepaid and deferred balances, and rollforwards; apply commission capitalization guidance (ASC 340-40) where applicable.
• - Own stock-based compensation and equity accounting under ASC 718: review SBC entries and equity rollforwards, and draft and maintain the equity footnote disclosures and supporting accounting memos.
• - Review benefits and other employee-related accounting, including worker’s compensation, health benefits, leaves, PTO, and 401(k) liabilities.
• - Own the 409A valuation process and international pension coordination.
• - Lead equity administration and compensation-system projects, such as the commission ASC 340 waterfall system adoption.

Financial Close, Controls, and Audit

• - Review payroll and compensation journal entries, balance sheet reconciliations, and GL account and financial statement flux analyses, communicating the activity and drivers behind each compensation-related account.
• - Apply strong GAAP and financial statement acumen to identify and propose accounting treatment for standard and non-standard compensation transactions, working with Technical Accounting on new or material matters.
• - Design, document, and maintain internal controls over payroll, bonus, SBC, and benefits in accordance with Sarbanes-Oxley.
• - Manage internal and external inquiries and prepare audit support for owned areas to successfully execute quarterly and annual financial statement audits.

Systems, Process Improvement, and Automation

• - Continuously improve the close task list, close calendar, and team close performance for the areas you own, reviewing how run-the-operation work gets done and solving operational inefficiencies at scale rather than simply getting the job done.
• - Partner with the AI & Automation function and use AI tools to streamline compensation accounting workflows, document repeatable processes, and make better use of the systems we already have.
• - Develop and maintain policies, procedures, and best practices that strengthen controls and team performance.

Leadership and Collaboration

• - Lead, coach, mentor, and train the team member(s) preparing payroll and compensation entries: set clear expectations and review standards, delegate effectively, and take an active interest in their career and development.
• - Partner with cross-functional teams within and outside of Finance, including Payroll, HR, Legal, Strategic Finance, and external auditors and vendors, to keep current on business priorities and build collaborative relationships.
• - Cross-train with fellow managers on other Corporate Accounting areas to build depth of coverage and process resilience across the team.
• - Own your area end to end with independent judgment, escalating to the Head of Corporate Accounting by exception.
• - Lead or assist on special projects as needed (e.g., process memos, compliance filings, systems implementations).
• - Ensure that all activities related to this position are accomplished in an ethical, prudent, and secure manner, particularly given the confidential nature of compensation data.

QUALIFICATIONS

• - 5+ years of related work experience. Big 4 or large regional public accounting firm experience is required, and at least 1 year of hands-on experience in a people manager or team lead role.
• - Strong working knowledge of US GAAP as it applies to compensation, including stock-based compensation (ASC 718), commissions and bonuses, and payroll-related accruals.
• - Hands-on experience with payroll, commission, and bonus accounting, with the ability to own the process end to end.
• - Strong MS Office Suite skills, including intermediate to advanced Excel (VLOOKUP, IF functions, pivot tables, etc.).
• - Analytical, skeptical, and curious; able to identify and report relevant risks and issues to management for timely and appropriate resolution.
• - Excellent organizational skills and attention to detail; proactively prioritizes tasks to meet deadlines and manages multiple projects in a fast-paced environment.
• - Highly organized and self-directed; drives issues and projects to resolution, follows through until they are closed, and clearly communicates and documents outcomes for leadership.
• - Concise and effective communicator with teammates, various levels of leadership, and external contacts; able to explain accounting topics clearly and logically.
• - Reliability with a strong work ethic, maturity, and professionalism to handle confidential data.

Nice to haves:

• - Prior experience at a SaaS and/or public company.
• - CPA license.
• - Experience with equity administration platforms (e.g., Carta), 409A valuations, and international pension or benefits accounting.
• - Experience with commission management tools and ASC 340-40 capitalization.
• - Proficiency using NetSuite with multi-entity and multi-currency, and experience with close management tools (e.g., Numeric or FloQast).
• - AI fluency: comfort using AI tools (e.g., Claude, Gemini) to improve productivity, analyze data, and streamline accounting workflows.

HOW WE WORK

We offer a flexible hybrid work arrangement that prioritizes in-office collaboration. Employees are expected to be on-site 3 days per week (Monday, Tuesday, and Thursday).

#LI-Hybrid

#BI-Hybrid

Benchling welcomes everyone.

We believe diversity enriches our team so we hire people with a wide range of identities, backgrounds, and experiences.

We are an equal opportunity employer. That means we don’t discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status. We also consider for employment qualified applicants with arrest and conviction records, consistent with applicable federal, state and local law, including but not limited to the San Francisco Fair Chance Ordinance.