Facility design challenges for small biopharma startups

For small biopharma startups, the leap from groundbreaking discoveries in the lab to full-scale drug production is both exhilarating and daunting. [Getty Images]
For all of the hurdles both compliance and technical rigor present for these companies, today’s potential is driven as much by investment as the desire to create life-changing medical advances. Through the CHIPS and Science Act, the designation of 31 innovation and technology hubs across the U.S. attracting more than $20 billion in private investment in biomanufacturing since 2022, market expansion for innovative startups brings incredible breakthroughs for the industry.
From scaling operations to ensuring regulatory compliance, every step requires thoughtful planning and execution. At the heart of this transition is the need for a well-designed facility that aligns with production goals while being adaptable, efficient, and up to code. Key challenges startups face in this journey include scaling operations, optimizing workflows, and meeting stringent industry standards.
Biomanufacturing facilities are not inexpensive to build, much less operate, and their costs can vary widely based on location, size, and the nature of the operations. While a facility in Sioux Falls, South Dakota, may be less costly to construct and operate than a facility in Boston or San José, the scarcity of labor may make such a facility challenging to staff. At the same time, a large facility, at scale, capable of reducing the costs per product, may be too much for a startup to operate daily. Utilities alone push budgets to meeting stringent ISO or GMP standards. Even benchmarking costs for startups can vex companies with the unique nature of each product manufactured influencing the final programming of the space.
Flexible lab designs offer effective solutions, enabling startups to navigate these complexities more easily while supporting long-term growth and success. While facility design lays the foundation for operational success, the inherent gap between discovery and production often poses significant challenges. Understanding and exploring these differences is critical to navigating the transition from research to manufacturing.
The gap between discovery and production
Biopharma startups typically begin with a strong focus on research and development, routinely prioritizing innovation over scalability. Laboratory methods optimized for precision and experimentation rarely translate seamlessly into production-scale workflows. As startups scale to meet market demand, they frequently encounter hurdles, including equipment incompatibilities, inefficient material flow, and regulatory shortcomings.
Unlike research labs, manufacturing facilities must accommodate large volumes of raw materials, ensure controlled environmental conditions, and optimize the movement of personnel and materials. Without a precise alignment between production processes and facility design, startups risk costly retrofits and compliance issues that can delay drug delivery to market and hinder getting medication into the hands of those who need it. To bridge this gap and address scalability challenges, startups increasingly turn to adaptable facility designs—an approach that offers flexibility and future-proofing.
Adaptable designs: A scalable solution
Adaptable facility design is emerging as a transformative solution for startups navigating this transition and allows for rapid assembly, reconfiguration, and expansion by detailing with standardized components. For instance, a company developing cell therapies might initially require small, controlled environments but later expand to larger bioreactors and additional quality control areas. Utilizing an adaptable facility design enables incremental growth, avoiding the upfront costs of oversized, underutilized spaces.
Additionally, adaptability provides agility in responding to regulatory changes. These designs can often be adjusted without significant downtime or disruption if a drug’s production requires stricter cleanroom classifications or unique containment measures. While adaptable designs offer scalability, optimizing workflows within these facilities is equally crucial to ensuring seamless output and efficiency.
Workflow optimization in facility design
Efficient workflows are critical to successful manufacturing. Poor facility layouts can lead to bottlenecks, contamination risks, and production delays—all serious concerns in the high-stakes biopharma industry. Startups must approach facility design with a holistic view of the production process, ensuring smooth movement of materials, personnel, and finished products. For example, strategically placing material entry points, processing areas, and storage spaces minimizes unnecessary movement and cross-contamination risks.
Adopting single-use systems, such as disposable bioreactors and tubing, is an example of how some decision-makers streamline workflows. These technologies reduce cleaning requirements, accelerate turnaround times, and mitigate contamination risks, allowing startups to focus on scaling production efficiently. Even with optimized workflows, startups must ensure their facilities adhere to strict regulatory standards—a challenge that requires early and comprehensive planning.
Regulatory compliance: A non-negotiable
Regulatory compliance is a formidable challenge for startups transitioning to manufacturing. Organizations like the Food and Drug Administration impose rigorous requirements on facility design, from aseptic environments and cleanroom classifications to equipment validation and documentation. Startups often need help both understanding and satisfying these standards, which demand niche technical expertise and substantial financial resources. It’s essential to integrate compliance considerations early into the facility design process to navigate these demands.
For example, HVAC systems must maintain appropriate air pressure differentials, while real-time monitoring systems ensure environmental conditions remain within acceptable ranges. Additionally, facility layouts should include spaces—quarantine, raw material sampling, and cold storage to name a few—for quality assurance and administrative tasks that support thorough documentation, a critical component of regulatory audits. Meeting compliance demands is a team effort that hinges on collaboration between startups, design professionals, and regulatory bodies.
Collaboration is key
Given the complexity of designing and building compliant manufacturing facilities, startups benefit significantly from collaboration with experienced professionals. Architects, engineers, and equipment vendors bring invaluable insights into facility requirements and emerging trends like continuous manufacturing, which integrates production steps into seamless workflows.
Engaging regulatory bodies early in the design process is another crucial step. Proactive feedback from regulators helps address potential compliance issues before construction begins, reducing the risk of costly revisions later. Collaboration also sets the stage for addressing critical challenges, such as optimizing space utilization and efficiency—a regular balancing act for resource-limited startups.
Space utilization and efficiency
Space constraints are a common startup challenge. Overestimating space needs can lead to financial strain while underestimating can result in inefficiencies. Adaptable lab designs help maximize space utilization by providing reconfigurable bench and production spaces.
For example, mobile workstations can enhance bench-top efficiency, accommodating changing production requirements without costly expansions. This strategy delays the need for more extensive facilities and ensures startups remain agile as they scale operations. Efficient space utilization goes hand in hand with process flow and flexibility, ensuring smooth transitions from research to production.
Process flow and flexibility

Transitioning from research to production often disrupts workflows, leading to inefficiencies and compliance risks. Process flow diagrams are powerful tools for visualizing how materials and personnel move through the facility. [Getty Images]
Designing facilities with efficient pathways that separate clean and dirty zones further enhances process flow. Adaptable walls and corridors also future-proof the space, accommodating transitions from single-use to reusable systems as production scales. These considerations become even more critical when adhering to cleanroom standards that ensure regulatory compliance.
Cleanroom standards: Building for compliance
Cleanroom compliance introduces complexities unfamiliar to many startups operating in unregulated lab environments. International Standards Organization (ISO) cleanroom standards require strict controls over airflow, material transfers, and cleanliness. Early planning is crucial to achieving compliance.
In multi-stage cleanroom environments, proper air pressure differentials, and material transfer protocols like airlocks or pass-through chambers must be incorporated into the initial designs. Such considerations streamline production while ensuring successful regulatory inspections. Understanding and integrating these standards seamlessly connects to cost considerations, an area where strategic investment can make or break a startup’s trajectory.
Cost considerations: Investing in the future
Startups often view facility costs as a barrier, prioritizing immediate savings over long-term value. However, cutting corners in facility design can result in higher operational inefficiencies, compliance issues, and costly retrofits. Investing in advanced systems, such as single-use technologies and real-time monitoring tools, provides significant long-term savings. For example, single-use systems reduce cleaning expenses and contamination risks, while monitoring tools enhance regulatory compliance and operational efficiency.
Educating stakeholders on these benefits through transparent cost-benefit analyses helps secure funding and investor buy-in for critical infrastructure investments. These cost-saving measures must be farsighted, ensuring facilities remain competitive in the evolving biopharma landscape
Future-proofing manufacturing facilities
Biopharma is rapidly evolving and driven by innovations like gene therapy and personalized medicine. Startups must design facilities that meet current needs while anticipating future demands. Design tools, such as BIM, allow teams to test facility layouts virtually, identifying potential issues before construction.
Advanced monitoring systems and data analytics further optimize facility performance, ensuring startups stay competitive in a dynamic landscape. Sustainability is also gaining traction in facility design. Energy-efficient systems, waste reduction strategies, and renewable energy sources reduce environmental impact and align with broader industry goals.
For small biopharma startups, the transition from research to manufacturing is pivotal. Success hinges on more than scientific innovation; it requires a facility that supports scalable, efficient, and compliant production. Adaptable, flexible lab designs offer practical solutions to these challenges, enabling startups to align facility capabilities with production goals while remaining adaptable to change. By prioritizing workflow optimization, regulatory compliance, and collaboration with industry experts, startups can confidently navigate this transition, bringing life-saving therapies to market more efficiently. In an industry where time and precision are critical, investing in thoughtful facility design is not just an advantage—it’s a necessity.

By prioritizing workflow optimization, regulatory compliance, and collaboration with industry experts, startups can confidently navigate this transition, bringing life-saving therapies to market more efficiently. In an industry where time and precision are critical, investing in thoughtful facility design is not just an advantage—it’s a necessity. [Getty]
Greg Verhoff, LEED AP, is the Business Leader for SSOE’s Pharma and Life Sciences sectors. He has nearly two decades of experience serving in the roles of construction manager, facility manager, and A/E project manager. His leadership provides a unique perspective that ensures SSOE’s design approach is achievable, maintainable, and cost-effective. His experience also includes serving as the architectural space planner and site master planner for a large pharmaceutical campus. He holds a Bachelor degree from The Ohio State University and is a founding member of the Lean Construction Institute’s Manufacturing Ecosystem Group (MEG). Greg can be reached at gverhoff@ssoe.com.
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