What Data to Collect From a Bioprocess Pilot Trial (Fermentation & Bioindustrial Scale-Up Guide)

Running a bioprocess pilot trial is one of the most expensive and time-intensive steps in scaling a fermentation or bioindustrial process. Pilot runs can take weeks or months to plan, yet the data generated during just a few days is used to inform critical scale-up, process design, and business decisions.

Despite this, very few startups I work with are able to immediately share all the relevant data from their pilot trial once it’s completed.

In most cases, some key information was never recorded, or the team has to go back to their scale-up partner weeks later, only to discover the data is missing, incomplete, or simply no longer available.

Why Pilot Trial Data Is Often Incomplete

This problem is rarely due to lack of effort or competence.

Bioprocess pilot trials are intense. Teams are focused on:

• getting the fermentation to run

• avoiding contamination

• hitting basic performance targets

• staying within time and budget

As a result, data that seems secondary during the run, operational details, utilities usage, deviations, and manual interventions often get overlooked. Unfortunately, these are exactly the data points that become critical after the pilot is over.

To make matters worse, formal pilot trial reports are often delivered weeks after the run, and by the time gaps are discovered, recovering that data can be slow or impossible.

Why This Matters for Scale-Up Decisions

Data from a fermentation or bioprocess pilot trial is used to inform:

• scale-up strategy and plant sizing

• process design and equipment selection

• cost and feasibility assessments

• investor updates and funding decisions

• planning the next pilot or demo run

Missing or incomplete pilot-scale data leads to:

• incorrect assumptions

• delayed decisions

• repeated pilot trials

• avoidable costs

In short, you only get one real chance to capture pilot data correctly.

A Lesson Learned From Real Pilot Trials

I’ve been responsible for dozens, if not hundreds, of bioprocess and fermentation pilot trials over the years.

Looking back, I genuinely wish I had a guide like this early in my career. In many cases, data wasn’t captured not because it wasn’t important, but because I didn’t yet know how important it would become later.

Experience teaches you one thing very clearly in scale-up work:

If it wasn’t written down during the run, it effectively doesn’t exist.

That’s the reason this guide exists.

My Number One Recommendation: Be Present at the Pilot Trial

If you can, send someone from your team to the pilot facility.

Yes, it might add a few thousand euros to the total cost of the pilot, but the learning and long-term value almost always outweigh that expense.

Being present allows you to:

• ask questions in real time

• capture operational details that never appear in reports

• document deviations, workarounds, and bottlenecks

• take photos, notes, and context that are invaluable later

If You Can’t Attend the Pilot Trial

If sending someone isn’t possible, make sure you explicitly agree in advance with your scale-up partner or pilot facility to:

• record and share raw bioreactor logs

• provide manual notes and operator observations

• capture photos of equipment, setup, and key steps

• share all raw data immediately after the pilot run

You can then wait for the formal pilot report when it’s issued weeks later, but you’ll already have the data secured for future analysis and decision-making.

A Practical Guide to Avoid Losing Critical Pilot Data

To help founders and technical teams avoid these issues, I’ve created a Pilot Trial Data Capture Checklist specifically for:

• fermentation pilot trials

• bioprocess scale-up runs

• bioindustrial pilot facilities

The checklist is designed to be used before, during, and immediately after a pilot run, ensuring that all relevant data is captured while it still exists.

Access the Checklist here:

Pilot Trial Data Capture Checklist