Biotech Financial Controller Job Description: When to Hire a Strategic Controller

Why Your Biotech Needs a Controller, Not Just an Accountant

In a biotech startup, the primary mission is scientific discovery. Managing finances often feels like a secondary task, with the CEO or COO handling the books alongside a fractional bookkeeper. This system, usually based on QuickBooks and spreadsheets, works for tracking a burn rate funded by grants and early investment. But as your company scales, this setup becomes a significant risk.

Preparing for a Series A audit, managing a major federal grant, or starting preclinical activities introduces financial complexities that demand specialized expertise. Hiring your first dedicated financial leader is a critical inflection point. The role you need is not just an accountant, but a strategic controller.

The most common mistake founders make is confusing the role of an accountant with that of a controller. An accountant is typically backward-looking, focused on recording historical transactions and ensuring basic compliance. A controller is a forward-looking system builder, responsible for creating the financial infrastructure that supports growth, manages risk, and provides strategic insight. The reality for most Seed to Series B startups is more pragmatic: you need one person who can do both, but their primary mandate must be to build, not just to record.

While an external accounting firm is excellent for tax returns, they are not embedded in your day-to-day operations. They will not build your clinical trial accrual process or manage the specific reporting for your government grants. A controller owns this entire financial engine, providing the internal leadership required for scaling.

Key triggers indicate it is time to hire. The ideal hiring time for a controller is three to six months before a major event like a Series A or B audit or the award of a significant grant. Another trigger is headcount. As you scale past 15-20 employees, the complexity of payroll, benefits, and operational expenses begins to outstrip the capabilities of a part-time bookkeeper.

We see the biotech controller role as having three distinct pillars:

• Defense (Compliance): Building an audit-ready financial foundation, ensuring meticulous grant compliance, and establishing pragmatic internal controls to protect company assets.
• Operations (Financial Engine): Managing the monthly close, overseeing accounting systems, and producing accurate, timely financial reports that guide leadership decisions.
• Strategy (Partnership): Collaborating with leadership on cash flow forecasting, budget management, and providing the financial data needed for fundraising and board meetings.

This framework helps define one of the most crucial biotech startup accounting roles and clarifies why you need a dedicated, in-house leader to navigate the unique financial challenges of the industry.

The Anatomy of a Biotech Controller Job Description

To attract the right candidate, your job description must reflect the unique challenges of a biotech startup. A generic controller description from another industry will not work. You must structure it around the specific, high-stakes responsibilities they will own. One of the most important biotech startup controller responsibilities is managing cash and compliance in a pre-revenue environment.

A compelling summary might read:

We are seeking a hands-on Financial Controller to build and lead our accounting function. You will be responsible for establishing an audit-ready financial foundation (Defense), managing our complex grant and clinical trial finances (Operations), and partnering with leadership to guide our financial strategy and extend our runway (Strategy).

Here are the core functional areas to detail in the job description.

1. Mastering Grant Compliance and Government Funding

For many biotechs, non-dilutive funding from government grants is a lifeline. However, this funding comes with strict compliance obligations. Mismanaging these funds is a key pain point for founders, as it can lead to clawbacks and jeopardize future grants. Your controller must be an expert in grant compliance for startups.

In the United States, the key regulation for managing federal grants is Uniform Guidance (2 CFR 200). A critical threshold is the 'single audit', which is triggered when an entity expends over $750,000 in federal grant funding in a fiscal year. Your controller must have deep experience with the rules set by common agencies like the National Institutes of Health (NIH) and the Department of Defense (DOD). They need to build systems to meticulously segregate and track direct versus indirect costs, a core requirement of grant management.

In the United Kingdom, the landscape is different but equally complex. The controller should have experience with grants from agencies like Innovate UK. They must also understand the specifics of claiming HMRC R&D tax credits, which requires rigorous tracking of qualifying expenditures to maximize the benefit.

2. Nailing Clinical Trial Finance and Accruals

As your company moves toward preclinical and clinical studies, financial management becomes exponentially more complex. The largest operational risk is mismanaging clinical trial accruals. Inaccurate forecasts can create unexpected cash shortfalls, potentially delaying trials and eroding investor confidence.

This is where the distinction between cash and accrual accounting is crucial. Your controller must master clinical trial financial management. A scenario we repeatedly see is this: a patient visit for a trial occurs in January. The contract research organization (CRO) might not send the invoice until March. A cash-basis bookkeeper would record the expense in March, distorting your monthly burn rate. Under accrual accounting, the controller must work with the clinical operations team to estimate and record that expense in January when it was incurred. This accuracy is vital for understanding your true R&D burn, forecasting cash needs, and reporting to investors.

3. Building an Audit-Ready Financial Foundation

Lacking audit-ready financials jeopardizes investor confidence and future fundraising. A controller's primary mandate is to build a financial function that can withstand scrutiny from investors, auditors, and regulators. This is a foundational aspect of biotech startup controller responsibilities and a key part of audit preparation biotech.

This process starts with clean bookkeeping. For US companies, financial statements must be prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP). In the UK, the standard is typically FRS 102. Your controller must own the integrity of these statements and ensure all external reporting requirements biotech are met.

Next are internal controls. For an early-stage company, this does not mean burdensome corporate bureaucracy. Instead, internal controls should be based on a pragmatic 'SOX-lite' framework, borrowing principles from the Sarbanes-Oxley Act. This means implementing right-sized controls like segregation of duties, formal vendor approval processes, and clear expense reimbursement policies.

Finally, the controller must manage your finance tech stack. Common tools include:

• Accounting: QuickBooks (US) or Xero (UK) for early stages, migrating to NetSuite.
• Cap Table: Carta.
• Bill Pay & Spend Management: Bill.com and Ramp.

A key responsibility for the controller will be to manage these systems and lead the eventual migration to a more robust Enterprise Resource Planning (ERP) system like NetSuite as the company's complexity grows.

The Ideal Candidate Profile: Must-Haves vs. Nice-to-Haves

Distinguishing between non-negotiable requirements and valuable additions is key to building the right biotech finance team structure and finding the perfect fit.

Must-Haves

• Active CPA License: This is a non-negotiable requirement for the role. It is the baseline indicator of technical proficiency, professional standards, and the ethical commitment required to build trust with investors and auditors.
• Industry-Specific Experience: Candidates must have 7+ years in accounting, with at least 3-5 years specifically in the biotech or pharmaceutical industry. Generalist controllers will not understand the nuances of grant accounting or clinical trial accruals.
• Technical Accounting Knowledge: Deep, hands-on expertise in U.S. GAAP for US-based roles or FRS 102 for UK roles. This is fundamental to producing compliant financial statements.
• Grant Accounting Experience: Proven experience managing government grants (e.g., NIH, DOD, or Innovate UK) and navigating their complex compliance and reporting requirements.

Nice-to-Haves

• Big 4 Public Accounting Experience: Experience with firms like Deloitte, PwC, EY, or KPMG is highly valued. This background provides a strong foundation in rigorous audit processes and internal controls, which is ideal for audit preparation biotech.
• ERP Implementation Experience: Experience leading a system migration from QuickBooks or Xero to an ERP like NetSuite is a significant plus, as this is a common transition for scaling startups.
• FP&A Skills: While the core role is accounting, experience with financial planning and analysis (FP&A) for budgeting and forecasting is a major advantage for strategic partnership.
• Capital Markets Experience: Familiarity with cap table management (using tools like Carta) and exposure to venture debt or IPO readiness processes can be valuable for a rapidly scaling startup.

Vetting Your Candidates: Questions That Reveal True Expertise

A resume can list qualifications, but scenario-based questions reveal a candidate's true problem-solving abilities and hands-on expertise. Move beyond standard interview questions and probe their understanding of core biotech startup controller responsibilities. Here are three questions designed to do just that:

1. On Grant Compliance: “We just received a large NIH grant. Walk me through the first 90 days of setting up our financial systems to ensure compliance with Uniform Guidance (2 CFR 200). What specific controls and reporting would you implement?”
2. A strong candidate will discuss setting up separate classes or projects in the accounting system, implementing time-tracking for personnel costs, distinguishing direct and indirect cost pools, and establishing a monthly grant reporting and reconciliation process to monitor the budget.
3. On Clinical Accruals: “Our CRO invoices are consistently 60-90 days late. How would you design a monthly accrual process to ensure our financial statements accurately reflect our clinical trial expenses in real-time? What data would you need from the clinical operations team?”
4. Look for answers that detail establishing strong communication channels with the ClinOps team, creating milestone-based or patient-based estimation models, and the specific journal entries required to book the accrual and reverse it when the actual invoice arrives. This demonstrates a deep understanding of accrual accounting.
5. On Systems Migration: “We are on QuickBooks but anticipate needing to migrate to NetSuite in the next 12-18 months. What are the key milestones you would establish for this project, and what are the biggest risks we should anticipate?”
6. A great answer will cover project phases like system selection, chart of accounts redesign, data validation and migration, and user acceptance testing and training. They should also identify risks like budget overruns, operational disruption during cutover, and ensuring data integrity post-migration.

Conclusion

Hiring your first financial controller is more than filling a back-office position; it is a strategic investment in your startup's future. The right person does more than close the books. They build the scalable financial infrastructure that de-risks your operations, instills investor confidence, and ultimately allows your scientific team to focus on its world-changing mission. Start by drafting a job description that focuses on the three pillars—Defense, Operations, and Strategy—to attract candidates who truly understand the unique financial landscape of a biotech startup.

For more on building your team, see our guide on sequencing finance hires.

Frequently Asked Questions

Q: What is the difference between a Controller and a VP of Finance?

A: A Controller is primarily focused on tactical and operational duties like closing the books, ensuring compliance, and managing internal controls. A VP of Finance is more strategic, focusing on fundraising, long-range financial planning, and investor relations. In an early-stage startup, a strong controller often handles aspects of both roles.

Q: Can I use a fractional controller for my biotech startup?

A: A fractional controller can be a good interim solution for very early-stage companies. However, as you approach clinical trials and manage significant grants, a full-time, in-house controller becomes essential for the deep operational integration required for accurate accruals and compliance.

Q: At what funding stage should I hire a controller?

A: The ideal time is typically after your Seed round and about three to six months before a Series A or B fundraise. This timing gives the controller enough runway to clean up the books, implement controls, and prepare the company for the intense financial due diligence of a major funding round.

Q: How do biotech startup controller responsibilities change if the company goes public?

A: For a public company, the controller role expands dramatically to include extensive SEC reporting duties (e.g., filing 10-Ks and 10-Qs) and managing rigorous Sarbanes-Oxley (SOX) compliance. The focus on internal controls, accuracy, and timeliness becomes even more critical due to public market scrutiny.