The Environmental Monitoring Gaps That Still Lead to Citations

Most facilities have an environmental monitoring (EM) program in place. But having a program is not the same as having one that actually works.

In recent inspections, FDA regulators have pointed out the same recurring issues. It’s not always about missing data, it’s about not using the data properly.

Inspectors are seeing EM systems that look fine on paper but don’t deliver when it comes to real-time control. Monitoring is being done but it’s not always meaningful.

The problem isn’t the lack of information. It’s the lack of action.

Turning EM Data Into Actionable Insights.

Where Things Often Go Wrong

Many of the issues inspectors raise are basic, and yet they keep turning up again and again.

Some of the most common problems include:

• Sampling locations that don’t reflect high-risk areas.

  
  

• No monitoring during critical production steps.

  
  

• Excursions that are logged but not properly investigated.

  
  

• Long-term trends that show problems, but no one follows up.

  
  

• Too many “0 CFU” results in areas where contamination is likely.

Inspectors no longer accept an EM program that simply checks the box. They expect to see a system that can detect contamination in real time, trigger the right response, and improve over time.

If you are collecting data and not using it, that’s a red flag.

Monitoring During Operations Still Missed

Both EU Annex 1 and FDA guidance are clear on this point: monitoring has to happen while operations are running. That includes viable and non-viable particle monitoring.

But even now, some facilities are only collecting samples before or after a batch, not during the most critical steps.

Annex 1 goes further and says that Grade A areas must have continuous non-viable monitoring during operations. It also expects near-continuous viable monitoring during production.

If your current setup can’t support that, it’s not just a space issue, it’s a design flaw. Inspectors will expect to see how you’ve addressed it or plan to fix it.

Investigations That Don't Go Deep Enough

When an EM excursion happens, it should start a clear investigation. Regulators expect a real root cause analysis.

Annex 1 states that all excursions must be investigated properly, even if they seem minor. Just repeating cleaning without knowing what caused the spike in contamination won’t satisfy inspectors.

They want to see that you’re asking the right question and using the answers to make improvements.

Trending is Not Just a Report

Most sites produce trend reports. The problem is what happens next. Often, the data is reviewed every few months, added to a slide deck, and then forgotten.

But trends are meant to inform decisions.

Annex 1 makes it clear that facilities should use EM trends to review and adjust alert and action limits, improve cleaning schedules, and update risk assessments.

If your reports show a slow increase in counts over several weeks or months, but nothing changes, that’s a gap. And it’s one inspectors will ask about.

Meaningful Monitoring, or Missed Opportunity?

An effective EM program is more than just collecting samples and printing reports. It needs to guide decisions and trigger real action.

Inspectors want to know: are you detecting problems early? Are you investigating them fully? And are you using that information to improve your controls?

If your EM data is not driving changes, it’s not doing its job. And regulators are more focused than ever on making sure environmental monitoring is meaningful.

When it isn’t, it becomes one of the easiest ways to get written up.

If Your EM Program Isn’t Driving Action, It’s Driving Risk

At Pharmalliance Consulting Ltd, we help manufacturers move beyond routine sampling to build environmental monitoring programs that actually support decision-making and meet regulatory expectations.

Our CPD-certified GMP Fundamentals Program includes practical guidance on EM design, investigation depth, and trend-driven improvement, so your monitoring doesn’t just look good on paper, it performs in practice.

Learn more and enrol here: pharmalliance.ie/gmp-fundamentals.

Because the data isn’t the problem, it’s what you do with it.