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How to Master Cleanroom Cleaning for Biotech Facility Compliance

by | Oct 25, 2024 | Biotech Cleaning, Cleanroom Cleaning, Pharmaceutical Cleaning

A scientist man injects a sample with a micro syringe into Mass Spectrometer

This blog was updated in Jan, 2026

Cleanroom cleaning plays a crucial role in maintaining the integrity of biotech facilities in the Bay Area. For companies operating in this high-stakes industry, ensuring a contamination-free environment is not just a requirement but a necessity for producing safe and effective products.

SourceOne Building Maintenance, a leading cleanroom janitorial company in the Bay Area, understands the unique challenges faced by biotech facilities and offers specialized services to meet stringent cleanliness standards.

To master cleanroom cleaning for biotech facility compliance, you need to understand the intricacies of cleanroom classifications, essential cleaning procedures and best practices for contamination control.

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Understanding Cleanroom Classifications for Biotech Facilities

To master cleanroom cleaning for biotech facility compliance, it’s crucial to understand the various classifications and standards that govern these controlled environments. Cleanroom classifications are based on the cleanliness level of the air inside the controlled environment, specifically the quantity and size of particles per cubic meter of air.

ISO Standards

The primary authority for cleanroom classifications in the United States and Canada is the ISO 14644-1 standard. This system includes classes ranging from ISO 1 (the cleanest) to ISO 9 (the least clean). Most biotech cleanrooms must comply with ISO Class 5 or lower, which is considered an extremely stringent classification standard.

ISO Class 5 cleanrooms allow a maximum of 3,520 particles per cubic meter that are 5 µm or larger. These facilities require frequent air changes to maintain their cleanliness level, with air velocity typically ranging from 40 to 80 feet per minute.

FDA and EC Requirements

The Food and Drug Administration (FDA) and European Commission (EC) have specific requirements for biotech facilities. These guidelines aim to ensure the safety, purity, and correct composition of sterile pharmaceutical products.

The FDA’s Good Manufacturing Practices (GMP) guidelines categorize sterile product manufacturing into four areas: Grade A, B, C, and D. These grades dictate the appropriate environment for producing sterile drugs and biological products.

Cleanroom Grades (A–D) and What They Mean in Practice

In sterile manufacturing and many life science environments, cleanroom “grades” are used to define how controlled an area must be based on the risk to the product. The higher the grade, the more sensitive the work being performed—and the more stringent the requirements for air quality, personnel practices, cleaning frequency, and environmental monitoring.
While ISO classifications describe airborne particle limits, cleanroom grades in sterile operations are often discussed in terms of where sterile product is exposed and how contamination could impact safety, quality, and compliance.

Grade A: The Critical Zone (Highest Control)

Grade A is the most controlled environment and is typically used for the highest-risk steps—where sterile product, sterile components, or open containers are exposed.
You’ll usually find Grade A conditions in areas such as:
  • aseptic filling lines (the point of fill)
  • open vial/stopper exposure points
  • sterile connections and transfers
  • aseptic compounding zones
This grade is commonly associated with ISO Class 5 conditions and requires extremely tight control over:
  • airflow patterns (often unidirectional/laminar airflow)
  • surface cleanliness at the point of use
  • rapid response to any excursion or abnormal monitoring result
Because Grade A is the “last line of defense” before product closure, cleaning here is not just frequent—it’s procedural, documented, and performed with materials and methods that minimize particle generation and residue.

Grade B: The Background for Aseptic Operations

Grade B areas typically serve as the background environment supporting Grade A operations. In other words, Grade B is designed to protect Grade A by controlling what surrounds it—especially during dynamic operations when people and materials are moving.
Grade B spaces often include:
  • aseptic processing rooms that house Grade A zones
  • gowning and staging areas that feed into critical suites (depending on facility design)
  • support areas where components are prepared before entering Grade A
You’ll often see Grade B described as meeting at least ISO Class 7 under dynamic conditions (when operations are running). The key point is that Grade B is still highly controlled, but the contamination risk is managed by combining:
  • strict gowning and personnel flow
  • disciplined material transfer procedures
  • cleaning schedules that match production cadence (including changeovers)

Grades C and D: Controlled, but Used for Lower-Risk Steps

Grades C and D are used for less critical stages of sterile product manufacturing—where the product is not as directly exposed, or where the process step is earlier and risk is lower.
Common examples include:
  • preparation steps prior to final sterile exposure
  • component staging and handling (depending on the process)
  • certain parts of formulation or equipment prep
  • support corridors and adjacent controlled spaces
In many facilities:
  • Grade C is often aligned with ISO Class 7 or ISO Class 8, depending on the specific operation and whether conditions are “at rest” or “in operation.”
  • Grade D is commonly aligned with ISO Class 8 for lower-risk controlled areas.
Even though these areas are “less critical,” they still matter. A contamination issue in Grade C or D can migrate into higher-grade zones through people, carts, materials, or airflow imbalances—so cleaning here is a foundational part of overall contamination control.

What It Takes to Maintain These Classifications

Cleanroom grades aren’t maintained by air filtration alone. Facilities typically rely on a layered contamination control strategy that includes:

1) Environmental Monitoring

Routine monitoring helps verify that conditions remain within specification. Depending on the area, this can include:
  • airborne particle counts
  • microbial monitoring (air and surface sampling)
  • pressure differentials between rooms
  • temperature and humidity control
Monitoring isn’t just “nice to have”—it’s what allows a facility to detect drift early and defend the state of control during audits.

2) Personnel Hygiene and Gowning Discipline

In cleanrooms, people are one of the largest contamination sources. Strong protocols reduce risk through:
  • validated gowning procedures
  • controlled movement patterns (to reduce turbulence and particle shedding)
  • training and periodic requalification
  • clear separation of “clean” vs “dirty” workflows

3) Air Filtration and Airflow Control (HEPA)

HEPA filtration is central to cleanroom performance. Properly installed and maintained HEPA filters can capture at least 99.97% of particles at 0.3 µm, and they support the airflow patterns needed to keep particles from settling on critical surfaces.
Just as important as the filter rating is the integrity and maintenance of the system—because damaged filters, poor seals, or unbalanced airflow can undermine an otherwise well-designed cleanroom.

4) Cleaning That Matches the Grade (and the Process)

Cleaning methods, tools, and frequencies should match the room classification and the operation. Higher-grade areas generally require:
  • low-lint, cleanroom-approved wipes and mops
  • controlled disinfectant use (and rotation when appropriate)
  • residue-aware techniques (so chemicals don’t interfere with processes)
  • documentation that supports audits and investigations

Why This Matters for Specialized Cleanroom Cleaning Providers

Understanding Grade A–D expectations is essential for companies like SourceOne Building Maintenance providing cleanroom cleaning services in the Bay Area. When cleaning teams align their procedures with the facility’s classification and contamination control strategy, they help clients protect:
  • product sterility and batch integrity
  • audit readiness and documentation quality
  • operational uptime and changeover efficiency
Ultimately, these standards exist for one reason: to ensure life science companies can produce safe, effective products in a controlled, defensible environment.

Essential Cleanroom Cleaning Procedures

To maintain the integrity of a cleanroom environment, it’s crucial to follow rigorous cleaning procedures. These procedures are designed to minimize contamination and ensure compliance with industry standards. Let’s explore the key aspects of cleanroom cleaning, including gowning protocols, surface cleaning and disinfection, and air quality management.

Gowning Protocols

Proper gowning is the first line of defense against contamination in a cleanroom. Before entering the cleanroom, personnel must follow a specific gowning procedure to minimize the introduction of particles. This process typically includes:

  1. Removing all personal items and jewelry
  2. Donning a bouffant cap to contain hair
  3. Washing hands thoroughly
  4. Putting on cleanroom-approved gloves
  5. Wearing a cleanroom hood and face mask
  6. Donning a cleanroom coverall
  7. Putting on cleanroom booties

It’s essential to ensure that all gowning components overlap properly to prevent any gaps where contaminants could enter. After gowning, personnel should use a mirror to perform a final check before entering the cleanroom.

Surface Cleaning and Disinfection

Maintaining clean surfaces is crucial for contamination control in cleanrooms. The cleaning process typically involves two steps: cleaning with a detergent followed by disinfection. Here are some key points to consider:

  • Use cleanroom-compatible cleaning agents and disinfectants
  • Start cleaning from the highest surfaces and work your way down
  • Employ a “pull-and-lift” technique when wiping surfaces to effectively remove contaminants
  • Use sterile, lint-free wipes or mops to avoid introducing new particles
  • Follow the manufacturer’s instructions for contact time to ensure effective disinfection

For ISO Class 5 or cleaner environments, it’s important to use sterile cleaning agents or sterile-filter them before use. Regular cleaning schedules should be established, with some tasks performed daily and others on a weekly or monthly basis.

Air Quality Management

Maintaining air quality is a critical aspect of cleanroom management. This involves:

  • Ensuring proper air changes per hour to continuously filter out particles
  • Using HEPA filters to remove 99.97% of particles 0.3 microns or larger 
  • Monitoring air pressure differentials between rooms to prevent contamination
  • Regularly inspecting and maintaining HVAC systems

By implementing these essential cleanroom cleaning procedures, facilities can maintain the high standards of cleanliness required for biotech and pharmaceutical operations. Regular training and adherence to these protocols are crucial for ensuring consistent compliance and product quality.

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Best Practices for Contamination Control

Maintaining a clean and controlled environment is crucial for biotech facilities to ensure product quality and compliance. To achieve this, it’s essential to implement best practices for contamination control. Let’s explore some key strategies to minimize the risk of contamination in cleanroom environments.

Personnel Training

One of the most critical aspects of contamination control is proper personnel training. Humans account for  in cleanrooms, shedding around 75% to 80% of particles 40,000 skin cells every minute. To address this, comprehensive training programs focused on Good Manufacturing Practices (GMP), proper hygiene practices, and contamination prevention are essential.

Training should cover topics such as:

  • Proper gowning procedures
  • Hand hygiene techniques
  • Cleanroom behavior and movement
  • Material handling protocols
  • Cleaning and disinfection procedures

Regular refresher courses are important to maintain high standards and adapt to any necessary changes. Engaging employees through interactive training sessions can help reinforce proper practices and prevent complacency over time.

Equipment Maintenance

Regular inspection and maintenance of cleanroom equipment are vital for preventing contamination. This includes tools, machinery, and instrumentation used in the cleanroom environment. To ensure the accuracy and reliability of synthesized products, all equipment should be calibrated at scheduled intervals.

Key aspects of equipment maintenance include:

  • Visual assessments to identify signs of wear, damage, or contamination
  • Calibration of devices that monitor environmental conditions and particle counts
  • Regular cleaning and disinfection of equipment surfaces
  • Proper storage or covering of equipment after each shift

Implementing a preventive maintenance schedule, rather than relying solely on breakdown maintenance, is critical to minimize the risk of contamination. This proactive approach helps identify potential issues before they lead to contamination events.

Material Handling

Proper material handling is essential to prevent the introduction of contaminants into the cleanroom environment. Implementing strict protocols for handling and storage of raw materials can minimize contaminant exposure related to the material’s stated requirements.

Best practices for material handling include:

  • Using cleanroom-compatible cleaning agents and disinfectants
  • Employing a “pull-and-lift” technique when wiping surfaces to effectively remove contaminants
  • Utilizing sterile, lint-free wipes or mops to avoid introducing new particles
  • Implementing proper storage practices, including dedicated locations on shelving and avoiding storage on floors
  • Ensuring all items have proper cGMP labels, including contents and expiration dates

By adhering to these best practices for contamination control, biotech facilities can maintain the high standards of cleanliness required for their operations. Regular training, equipment maintenance, and proper material handling are key components of an effective contamination control strategy, helping to ensure product quality and regulatory compliance.

Monitoring and Maintaining Cleanroom Compliance

To ensure the highest standards of cleanliness and regulatory compliance in biotech facilities, it’s crucial to implement robust monitoring systems and maintain meticulous records. This section will explore the key aspects of monitoring and maintaining cleanroom compliance, including environmental monitoring systems,  documentation practices, and regular audits.

Environmental Monitoring Systems

Environmental monitoring is a critical component of cleanroom management, helping to reduce the risk of out-of-specification conditions and keep facilities audit-ready and compliant. These systems continuously measure and record various parameters essential for maintaining the cleanroom’s integrity.

Key aspects of environmental monitoring include:

  1. Air Quality Metrics: Particle counters should be used to measure amounts of particulate matter down to 0.1 microns or even below. Readings should be taken at multiple locations around the cleanroom to identify localized issues.
  2. Air Changes per Hour: In ISO class 1 cleanrooms, monitoring air changes per hour is crucial to ensure positive pressure and adequate filtration.
  3. Temperature and Humidity: These parameters should be consistently monitored and controlled to maintain optimal conditions for cleanroom operations.
  4. Differential Pressure: Measuring pressure differences across filter banks and between rooms helps prevent contamination from adjacent areas.
  5. Microbial Testing: Regular testing for microbial contamination is essential to ensure the cleanliness of the room.

Implementing a comprehensive environmental monitoring system can help integrate various measurements and provide real-time data on cleanroom conditions.

Documentation and Record Keeping

Maintaining accurate and detailed records is crucial for demonstrating compliance with regulatory requirements and internal standards. Proper documentation practices include:

  1. Standard Operating Procedures (SOPs): Develop and maintain up-to-date SOPs for all cleanroom operations, including cleaning protocols, gowning procedures, and monitoring processes.
  2. Maintenance Records: Keep detailed records of equipment maintenance, calibration, and repairs.
  3. Environmental Monitoring Data: Document all environmental monitoring results, including particle counts, microbial testing, and other relevant parameters.
  4. Training Records: Maintain records of personnel training on cleanroom protocols and procedures.
  5. Incident Reports: Document any deviations from standard procedures, contamination events, or other incidents, along with the corrective actions taken.
  6. Audit Reports: Keep records of internal and external audits, including findings and follow-up actions.

Ensure that all documentation is clear, legible, and easily accessible for review during audits. Implement a system for regular review and updating of documents to reflect any changes in procedure or regulatory requirements.

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Regular Audits and Inspections

Conducting regular audits and inspections is essential for maintaining cleanroom compliance and identifying areas for improvement. Key aspects of this process include:

  1. Internal Audits: Perform routine internal audits to assess compliance with SOPs and regulatory requirements. These can be conducted quarterly or bi-annually, depending on the facility’s needs.
  2. External Audits: Schedule annual or bi-annual audits by regulatory agencies or certifying bodies to ensure compliance with industry standards.
  3. Supplier Audits: Conduct yearly audits of suppliers and contract manufacturers to ensure they meet the necessary requirements.
  4. Pre-Audit Preparation: Before external audits, conduct internal pre-audits to identify and address potential issues proactively.
  5. Corrective Actions: Implement a system for tracking and addressing any non-conformities identified during audits.
  6. Continuous Improvement: Use audit findings to drive ongoing improvements in cleanroom operations and procedures.

By implementing robust environmental monitoring systems, maintaining meticulous documentation, and conducting regular audits, biotech facilities can ensure ongoing compliance with cleanroom standards and maintain the highest levels of product quality and safety.

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Ensuring Cleanroom Compliance

Mastering cleanroom cleaning for biotech facility compliance is a multifaceted process that has a significant impact on product quality and safety. By understanding cleanroom classifications, implementing essential cleaning procedures, and following best practices for contamination control, facilities can maintain the stringent standards required in the biotech industry. SourceOne Building Maintenance, a leading cleanroom janitorial company in the Bay Area, plays a crucial role in helping local biotech companies achieve and maintain these high standards of cleanliness and compliance.

Effective monitoring and maintenance of cleanroom compliance are essential to ensure ongoing adherence to regulatory requirements. This involves implementing robust environmental monitoring systems, maintaining meticulous documentation, and conducting regular audits. By prioritizing these aspects, biotech facilities in the Bay Area can stay ahead of potential issues and continuously improve their operations. To get expert assistance in maintaining your cleanroom’s integrity and compliance, reach out to SourceOne Building Maintenance for their specialized cleanroom cleaning services.