Top 10 Cleanroom Cleaning Mistakes That Lead to FDA Audit Findings
In GMP-regulated industries like pharmaceuticals, biotech, life sciences, and medical device manufacturing, the cleanroom is the heart of compliance. A single cleaning mistake in a cleanroom can cause contamination, slow down production, or even trigger an FDA audit finding that damages both reputation and revenue.
Unfortunately, many facilities — even those with strong quality systems — still fall into the same common cleanroom cleaning mistakes. The good news is, once you know what they are, you can prevent them.
In this post, we’ll break down the top 10 cleanroom cleaning mistakes that lead to FDA audit findings, and how to avoid them.
1. Using Untrained Personnel
One of the biggest mistakes facilities make is letting untrained or under-trained staff clean GMP cleanrooms. Regular janitorial companies often don’t understand ISO cleanroom cleaning standards, GMP compliance, or contamination control.
Why it matters: Untrained cleaners shed particles, use the wrong tools, and skip key steps. FDA auditors can spot this instantly.
How to fix it: Use certified cleanroom cleaners or train your staff through a cleanroom training program that teaches proper gowning, wiping, and cleaning techniques.
2. Poor Gowning Practices
Even before cleaning starts, improper gowning procedures create contamination risks. A single exposed hair or a poorly fitted mask can release thousands of particles into the controlled environment.
Why it matters: Gowning errors are one of the first things auditors look for when reviewing cleanroom compliance.
How to fix it: Train cleaners on ISO-compliant gowning protocols and enforce them with regular audits.
3. Not Following a Top-to-Bottom, Clean-to-Dirty Method
Many cleaners wipe surfaces randomly or in the wrong order. In a cleanroom, cleaning must always move from cleanest to dirtiest areas and from top to bottom.
Why it matters: If you clean floors before ceiling vents, you’ll recontaminate the room.
How to fix it: Follow a standardized SOP that clearly defines the cleaning sequence: ceilings → walls → surfaces → equipment → floors.
4. Using the Wrong Wiping Technique
Scrubbing in circles or reusing contaminated wipes spreads particles instead of removing them.
Why it matters: Improper wiping leaves residues and increases microbial contamination risk.
How to fix it: Train staff to use the one-directional, overlapping wipe method with approved lint-free wipes.
5. Incorrect Use of Disinfectants
Using household cleaners, mixing chemicals incorrectly, or failing to rotate disinfectants are all major mistakes.
Why it matters: The FDA expects validated, GMP-approved disinfectants like 70% isopropyl alcohol, and expects rotation to prevent microbial resistance.
How to fix it: Follow your facility’s SOP for approved disinfectants, and ensure cleaners understand how to prepare and apply them properly.
6. Lack of Documentation
In cleanrooms, if it isn’t documented, it didn’t happen. Too often, staff forget to log a cleaning activity, or logs are incomplete.
Why it matters: During an FDA audit, missing documentation is treated as non-compliance — even if the cleaning was performed.
How to fix it: Use digital documentation systems or detailed paper logs to ensure every cleaning step is traceable.
7. Talking, Eating, or Rushing in the Cleanroom
Every time someone talks loudly, eats, chews gum, or runs inside a cleanroom, they release thousands of particles into the air.
Why it matters: Particle control is the foundation of ISO 14644 compliance. Auditors will note if personnel behavior violates this.
How to fix it: Train cleaners and operators on cleanroom etiquette: move slowly, avoid unnecessary talking, and never bring food or drink inside.
8. Using Non-Approved Tools
Household mops, cotton cloths, or non-sterile sponges have no place in a GMP cleanroom.
Why it matters: Non-approved tools shed fibers, hold contaminants, and leave residues that auditors will quickly notice.
How to fix it: Use validated cleanroom cleaning tools like microfiber mops, HEPA vacuums, and lint-free wipes designed for controlled environments.
9. Outdated or Incomplete SOPs
Standard Operating Procedures (SOPs) for cleaning must be current, detailed, and tailored to your facility. Many companies rely on generic SOPs that don’t reflect actual processes.
Why it matters: FDA auditors will review SOPs against real-world cleaning practices. If they don’t match, it’s a finding.
How to fix it: Regularly update your SOPs and ensure they reflect your GMP and ISO cleanroom cleaning protocols.
10. Treating Cleanroom Cleaning as “Housekeeping”
The biggest mistake of all is thinking cleanroom cleaning is the same as janitorial work.
Why it matters: Cleanroom cleaning is a compliance function tied to patient safety and audit readiness. Undervaluing it creates risk at every level.
How to fix it: Invest in professional cleanroom cleaning services, training, and certification programs that emphasize regulatory compliance.
Why These Mistakes Matter to QAs and QMs
If you’re a Quality Assurance or Quality Manager, you know that FDA and ISO audits always review cleaning procedures, SOPs, and training records. Every one of these 10 mistakes is a potential audit finding, CAPA, or even product recall.
This is why more companies are working with specialized providers who understand the compliance side of cleaning. At Controlled Environmental Custodians, we:
Train and certify cleanroom cleaners through our online LMS platform
Develop and update SOPs tailored to your facility
Provide mock cleanroom training so staff can practice in a controlled setting
Offer audit support and documentation tools for QAs and QMs
The goal is simple: eliminate the mistakes that lead to FDA findings and keep your cleanroom in full compliance.
Final Thoughts
The cleanroom is not just a space — it’s a controlled environment that protects patients, products, and your business. Too many facilities still make these 10 common cleanroom cleaning mistakes, and every one of them increases the risk of an FDA finding.
By investing in proper training, documentation, and cleanroom cleaning services, you protect not only your compliance status but also the integrity of every product that leaves your facility.
If you’re ready to eliminate cleaning mistakes and strengthen your compliance program, reach out to Controlled Environmental Custodians today. We’ll help you build a cleanroom cleaning program that is audit-ready, FDA-compliant, and contamination-free.