Clean rooms in the pharmaceutical industry: The complete setup guide
Clean rooms in the pharmaceutical industry are the foundation of safe, compliant, and high-quality drug development and manufacturing. From early-stage research to commercial-scale production, clean environments protect products, processes, and people. They help pharmaceutical companies meet strict regulatory standards while maintaining consistency and efficiency.
If you’re in biopharma and are planning a new facility or upgrading an existing one, setting up a pharmaceutical clean room can be complex and feel overwhelming. There are regulatory requirements to meet, design decisions to make, and long-term operational goals to consider. This guide walks you through the complete setup process in a clear and practical way, so you can make informed decisions at every stage.
At PodTech™, we work with pharmaceutical companies that need reliable, scalable clean room solutions. This article reflects the same thoughtful and practical approach we employ across all our projects.
Why clean rooms matter in the pharmaceutical industry.
Clean rooms in the pharmaceutical industry exist for one primary reason: control. Pharmaceutical products are highly sensitive to contamination from particles, microorganisms, and even people. A clean room creates a controlled environment where these risks are minimised.
Pharmaceutical clean rooms support:
- Product safety and patient health
- Regulatory compliance with global standards
- Process consistency and repeatability
- Protection of high-value research and manufacturing activities
Without properly designed and maintained clean rooms, pharmaceutical operations face increased risks of batch failures, recalls, and regulatory penalties. In an industry where trust and precision are essential, clean rooms are not optional. They are a core requirement.
What defines a pharmaceutical clean room? Understanding the fundamentals.
A clean room is a controlled environment with defined limits on airborne particles, temperature, humidity, pressure, and microbial contamination. In the pharmaceutical industry, clean rooms are designed to meet specific classifications based on how clean the air must be.
Clean room classifications. Clean rooms are commonly classified using ISO standards, which range from ISO Class 1, the cleanest, to ISO Class 9. Pharmaceutical clean rooms typically fall within ISO Class 5 to ISO Class 8, depending on the process.
For instance, ISO Class 5 cleanrooms are often used for aseptic filling and critical operations. ISO Class 7 is common for compounding and preparation areas, while ISO Class 8 may be used for support areas and less critical processes.
Each classification defines the maximum number of particles permitted per cubic metre of air. The cleaner the room, the more advanced the filtration and airflow systems need to be.
Key environmental controls. Clean rooms in the pharmaceutical industry rely on several interconnected systems:
- High efficiency particulate air (HEPA) filters to remove airborne contaminants
- Controlled airflow patterns, often laminar flow
- Precise temperature and humidity regulation
- Pressure differentials to prevent cross contamination
- Smooth, cleanable surfaces that do not shed particles
All of these elements work together to create a stable and predictable environment.
Regulatory standards and compliance requirements. Regulatory compliance is one of the most important drivers of clean room design in the pharmaceutical industry. Authorities around the world expect pharmaceutical clean rooms to meet strict guidelines.
Some of the most common standards include:
- Good Manufacturing Practice (GMP) guidelines from agencies such as the FDA and EMA
- ISO 14644 standards for clean room classification and testing
- Annex 1 of EU GMP for sterile medicinal products
- Local health authority requirements depending on location
These regulations cover everything from clean room design and materials to monitoring, validation, and ongoing maintenance.
Validation and documentation. Clean rooms in the pharmaceutical industry must be validated before use and regularly revalidated over time. Validation typically includes installation qualification (IQ) to confirm systems are installed correctly, operational qualification (OQ) to verify performance under operating conditions, and performance qualification (PQ) to ensure consistent results during real processes.
Documentation is critical. Regulators expect detailed records of design decisions, testing results, and ongoing monitoring. Working with an experienced clean rooms manufacturer can simplify this process and reduce compliance risks.
Planning your clean room setup.
A successful clean room project starts with careful planning. So, before choosing a design and construction method, it is important for you to clearly define your needs.
For starters, you must define your processes and workflows. Start by mapping out what activities will take place in the clean room. Consider the type of products being handled, the level of cleanliness required for each process, material and personnel flow, and equipment size and layout needs. Clear workflows help prevent cross contamination and improve efficiency. They also influence the size, layout, and classification of each clean room zone.
You must also consider future growth. Pharmaceutical operations often evolve. New products, increased production volumes, or regulatory changes may require adjustments in the future. Planning for flexibility from the beginning can save time and cost later. This is one reason why modular clean rooms and prefabricated clean rooms have become increasingly popular: they allow facilities to expand or reconfigure without major disruption.
Modular and prefabricated clean rooms vs traditional solutions.
One of the biggest decisions in clean room setup is choosing between traditional construction and modern modular approaches.
Traditional clean rooms are built on-site using conventional construction methods. They are often custom designed for a specific space. They boast of advantages like a high level of customisation and seamless integration into existing structures.
However, traditional construction also comes with challenges. Think longer build times, higher labour costs, limited flexibility for future changes, and disruption to existing operations.
Modular clean rooms, on the other hand, are built using pre-manufactured components that are assembled on-site. Walls, ceilings, and systems are designed to fit together precisely. It’s no surprise, then, that modular clean rooms boast of faster installation timelines, more predictable costs, easier upgrades and reconfiguration, and consistent quality that comes from controlled manufacturing. They offer a faster path to validation and operation without compromising on quality, timelines, or budgets.
For many pharmaceutical companies, modular clean rooms offer the right balance between customisation and efficiency. At PodTech™, prefabricated and modular solutions are often ideal for pharmaceutical clients who need speed, scalability, and compliance without compromise.
In part two of this blog post, we’re going to explore the key design elements of pharmaceutical clean rooms, from zoning to air filtration. We’ll also shed light on other critical steps in the pharmaceutical clean room setup process. So, if setting up a cleanroom for your biopharma business is on the cards, stay tuned for the rest of this guide; it’s sure to help you make a well-considered decision.
Now that we’ve covered the basics of clean rooms in the pharmaceutical industry in part one, let’s move on to clean rooms manufacturers, design elements, operations, and maintenance.
Form and function: Key design elements of pharmaceutical clean rooms.
Designing clean rooms in the pharmaceutical industry requires keen attention to detail. Every element impacts performance and compliance.
Layout and zoning. Pharmaceutical clean rooms are typically divided into zones based on cleanliness levels. Higher grade areas are protected by surrounding lower grade spaces. Proper zoning helps maintain pressure differentials, control contamination risks, and support logical workflows. Personnel and material entry points should be clearly separated and supported by airlocks or pass through systems.
Materials and finishes. Surfaces in pharmaceutical clean rooms must be easy to clean, durable, and resistant to chemicals. Common features include smooth, non-porous wall panels, seamless flooring with coved edges, flush mounted lighting and fixtures, and minimal joints and crevices. These features reduce particle accumulation and simplify cleaning and disinfection.
HVAC and filtration systems. The HVAC system is the heart of any clean room. It controls air quality, temperature, humidity, and pressure. When selecting an HVAC system, key considerations include HEPA or ULPA filtration efficiency, air change rates appropriate for the clean room class, laminar or turbulent airflow design, and redundancy for critical systems. A well-designed HVAC system supports both compliance and comfort for personnel.
You’re only as good as your partner: Selecting the right clean rooms manufacturer.
Choosing the right clean rooms manufacturer is one of the most important decisions in your setup process. The right partner brings expertise, reliability, and a clear understanding of pharmaceutical requirements.
Wondering what to look for in a clean rooms manufacturer?When evaluating potential partners, consider their experience with pharmaceutical clean rooms. Assess their knowledge of regulatory standards, ability to deliver modular and prefabricated clean rooms if that’s what you need, project management and validation support, and long-term service and support capabilities.
A manufacturer that understands your industry can anticipate challenges and provide solutions that align with your goals.
The value of an integrated approach. Working with a clean rooms manufacturer that offers design, fabrication, installation, and validation support simplifies communication and reduces risk. It also helps ensure that all components work together as intended.
PodTech™ takes this integrated approach, helping pharmaceutical companies move from concept to operation with confidence.
Facility manufacturing isn’t the end: The role of installation, commissioning, and maintenance.
Once design (and off-site manufacturing, for modular clean rooms) are complete, construction (or installation) and commissioning bring your clean room to life.
Installation best practices. If you’re going the prefab or modular route, efficient installation depends on careful coordination and planning. Since many components arrive ready to assemble, key installation considerations include coordinating schedules, minimising disruption to any existing operations, ensuring proper sealing and correct alignment, and maintaining a level of cleanliness that is acceptable given cleanroom standards. Experienced installers and clear procedures are not negotiable.
Commissioning and validation. Commissioning verifies that all systems operate as designed. This includes testing airflow, filtration, temperature, humidity, and pressure. Validation follows commissioning and confirms that the clean room consistently meets required standards. This step is critical for regulatory approval and operational readiness.
Operating and maintaining pharmaceutical clean rooms.
Setting up clean rooms in the pharmaceutical industry is only the beginning. Ongoing operation and maintenance are just as important to ensure continued cleanliness and compliance.
Cleaning and disinfection protocols. Regular cleaning and disinfection are essential to maintain clean room performance. Protocols should be clearly defined, validated, and documented. You have to make decisions about frequency of cleaning tasks, approved cleaning agents, personnel training, and monitoring. Consistency and discipline are key to long term success.
Environmental monitoring. Continuous or routine monitoring helps detect issues before they become problems. Monitoring may include particle counts, microbial sampling, temperature and humidity tracking, and pressure differentials. The data collected from monitoring programs supports compliance and continuous improvement.
Training and behaviour. Even the best designed clean room can be compromised by poor practices. That’s why personnel training is critical. Your training programmes should cover gowning procedures, acceptable clean room behaviour, material handling, and response to deviations. You must also build a culture of quality and accountability; this is a critical factor supporting clean room performance over time.
Common challenges and how to address them.
Pharmaceutical clean room projects often face challenges. Understanding them early helps you plan effectively.
Balancing cost and compliance. Clean rooms are a significant investment. The goal is not to cut corners, but to make smart decisions that deliver value. Modular and prefabricated clean rooms can reduce construction time and costs while maintaining compliance.
Managing timelines. Delays in clean room projects can impact product launches and research milestones. Choosing experienced partners and proven systems helps keep projects on track.
Adapting to change. Regulations, products, and processes evolve. Flexible clean room solutions make it easier to adapt without major renovations.
The future of clean rooms in the pharmaceutical industry.
The pharmaceutical industry continues to innovate, and clean room technology evolves alongside it.
From advanced monitoring and automation to greater energy efficiency and sustainability, from increased use of modular and prefabricated clean rooms to faster deployment for emerging therapies and urgent needs, diverse trends are shaping the future.
Clean rooms in the pharmaceutical industry are becoming more adaptable, efficient, and integrated with digital systems. If you want to remain competitive in the biopharma market, you have no option but to keep up. Companies that invest in flexible solutions today will be better prepared tomorrow, when regulations, standards, and market demand change.
Why PodTech™ is a trusted partner for pharmaceutical clean rooms.
Clean rooms in the pharmaceutical industry are essential to delivering safe and effective products to patients around the world. A successful setup requires careful planning, informed design choices, and the right partners.
By understanding regulatory requirements, exploring modular and prefabricated clean rooms, and working with an experienced clean rooms manufacturer, you can build environments that support both compliance and innovation.
PodTech™ is a trusted partner for pharmaceutical clean rooms. At PodTech™, we understand the unique challenges of pharmaceutical environments. Our focus on modular and prefabricated clean rooms allows us to deliver solutions that are compliant, scalable, and efficient. Our clients choose us because we offer deep expertise in pharmaceutical clean rooms, high-quality manufacturing and materials, faster project timelines, support from design through validation, and a collaborative and transparent approach.
Our goal is to help you create clean rooms that support your research, protect your products, and grow with your organisation. If you are considering a new clean room or upgrading an existing facility, PodTech™ is here to help. Reach out to learn more about our approach and how we support pharmaceutical teams at every stage of their journey.