Pilot-Scale Labs: Equipment Planning Tips & Mistakes to Avoid

Pilot-scale labs aren’t just “R&D, but bigger.” They’re the proving ground where your science meets real-world demands—process validation, regulatory prep, and tight quality control. Unlike the controlled chaos of bench-scale experiments, pilot-scale work demands repeatability and scalability, all under the watchful eye of investors and regulators.

Why does this transition trip up even experienced teams? Unlike the controlled chaos of early lab-scale or bench-scale work, pilot-scale operations demand repeatability, regulatory viability, and scalability—all under the watchful eye of investors, regulators, and future partners. Poor equipment planning at this stage isn’t just an inconvenience; it can mean costly downtime, failed batches, or delays that threaten your next funding milestone.

Ask yourself: Are you ready for the operational leap from small scale to something approaching commercial scale, or are you about to discover your “must-have” gear only after a critical process stalls? If you’re feeling the pressure, you’re not alone. Many biotech founders and lab managers find themselves navigating a maze of procurement decisions, process optimization goals, and shifting operating parameters—all while keeping burn rate and runway in mind.

In this quick guide, we’ll break down practical ways to plan your pilot-scale equipment, highlight common mistakes (so you can avoid them), and share operator-level insights to help you build a lab that’s efficient and cost-effective from day one. Whether you’re a founder, lab manager, or finance lead, you’ll find strategies to keep your setup lean, scalable, and ready for whatever comes next.

Define Your Pilot-Scale Goals Before Buying Equipment

Before you start drafting purchase orders or comparing specs, it’s worth stepping back to clarify what you actually need your pilot-scale lab to accomplish. This isn’t about slowing things down—it’s about making sure every dollar, square foot, and raw material is working toward your next milestone.

The reality is that “pilot scale” can mean different things depending on your company’s stage and process design objectives. Maybe you’re gearing up for process validation, or you’re preparing for GMP compliance. Some teams need to produce clinical-grade material, while others are focused on generating enough data from pilot studies or scale experiments to get a partner or investor over the line.

Each scenario shapes your equipment priorities in a big way:

• If GMP is on the horizon, documentation, control of process parameters, and system validation will influence which providers and systems make the cut.
  
• If you’re running demo batches to test new formulations or simulate real-world conditions, flexibility and quick turnaround might trump full automation or scale.
  
• If you’re supporting multiple programs or new technologies, modularity and future-proofing may matter more than buying the biggest reactor you can afford.
  

Getting specific about your goals helps you avoid two common traps: overbuying (spending on capabilities you won’t use for a year or more) and under-spec’ing (realizing too late that your setup can’t support larger-scale workflows).

A practical approach: sketch out your next 12–24 months. What do you need to deliver, and when? Where are the inflection points—like a regulatory submission or a key partnership—that might change your requirements?

Bringing your team (including chemical engineering, finance, and facilities leads) into this conversation early pays off. It keeps everyone aligned and helps you make tradeoffs with eyes wide open, rather than reacting to surprises when you scale up.

Core Equipment Needs in a Pilot-Scale Environment

Once your goals are clear, you can start translating them into a practical equipment list. The shift from laboratory scale to pilot scale isn’t just about sizing up; it’s about building a system that can handle larger-scale operating conditions without becoming overcomplicated or underpowered.

Here’s what most teams find themselves evaluating:

1. Bioreactors and Fermenters

The heart of many pilot plants, these systems come in a range of volumes and control capabilities. Think about:

• Batch size: What’s your minimum viable run, and what’s the upper flow rate or volume you might need in the next year?
  
• Modularity: Can you swap vessels or change configurations as your methodology evolves?
  
• Automation: How much hands-on time can your team realistically support at this scale?
  

2. Downstream Purification Systems

Pilot-scale means larger volumes and more complex separation steps. You’ll likely need:

• Chromatography skids: Scalable columns and pumps for protein, small molecule, or biomass purification.
  
• Filtration systems: Tangential flow filtration (TFF) or similar setups, sized for your expected throughput and aligned with your process scalability goals.
  

3. Analytical Instrumentation

Quality assurance becomes critical at this stage. Consider:

• HPLC/UPLC: For purity and identity testing of your chemical process outputs.
  
• Mass spectrometry: For detailed characterization, especially when developing new products.
  
• Automation or sample handling: To keep up with high sample variability and load.
  

4. Supporting Infrastructure

Often underestimated, these systems can make or break your production process:

• HVAC: Must support stable operating conditions for sensitive reactions and equipment.
  
• Cold storage: Think upright freezers, walk-in cold rooms, or liquid nitrogen systems for temperature-sensitive materials.
  
• Process water and drainage: Type I/II systems and proper wastewater treatment or disposal capacity.
  
• Utilities: Sufficient power, gas lines, and compressed air for your full-scale operations and future growth.
  

5. Flexibility and Future-Proofing

If your pipeline or formulations are still evolving, consider:

• Mobile workstations or modular benches: For adapting your layout to new workflows.
  
• Extra utility drops: To make adding new tools, reactors, or instruments easier.
  
• Space for expansion: Don’t max out your facility on day one; build with future scalability in mind.

Operator insight: The “invisible” systems—like HVAC, drainage, and utilities—are often the bottlenecks that stop larger-scale production from running smoothly. Don’t wait until installation day to discover a mismatch between your equipment and facility capabilities.

Mistakes to Avoid When Planning Your Setup

Even with a solid plan, it’s easy to hit unexpected snags when moving to pilot scale. The difference between a smooth transition and a string of costly delays often comes down to avoiding a handful of classic mistakes. Here are the big ones to watch for:

1. Buying Before Protocols or Throughput Needs Are Finalized

It’s tempting to get ahead of long lead times by ordering equipment early. But if your process isn’t locked down, you risk ending up with gear that doesn’t match your actual production process—or, worse, can’t support your targeted flow rate, chemical reaction conditions, or process parameters.

Reality check: Has your team run enough pilot studies or scale experiments to know what “typical” looks like under real-world conditions? If not, it might pay to hold off—or look for flexible options like leasing or modular systems—until the methodology is more defined.

2. Overlooking Facility Constraints

Floor load, ceiling height, door width, venting, and access to utilities—these details can make or break your scale-up plan. One example: More than one startup has discovered on delivery day that their new reactor or centrifuge won’t fit through the door, or that the floor can’t handle the full load of a larger-scale setup.

Tip: Walk the space with your facilities lead and tape out equipment footprints. Account for things like evaporation, heat transfer, and airflow—especially if your process generates heat or moisture.

3. Ignoring Service and Maintenance Access

It’s easy to pack a room for maximum capacity, but if a technician can’t reach the back of your chromatography skid or perform validation checks, you’re asking for trouble.

Tip: Plan for at least 3 feet of clearance around large equipment, and make room for carts, waste collection, and routine servicing of pumps, vessels, and instrumentation.

4. Overfitting to a Single Pipeline

Customizing your setup around one formulation or target compound might feel efficient—but it can box you in if your product strategy changes, or if you shift from lab scale to industrial scale production. Consider this: Can your current systems handle changes in raw materials, formulations, or scale-up to a full-scale plant? Could your workflow accommodate new technologies, or a pivot from chemical to biologic processes?

Future-proofing means that, whenever possible, choose multi-purpose or modular systems that can adapt across different scales, from pilot to commercial production.

Quick gut-check: If your science or business model changed tomorrow, how much would you need to rip out and replace?

Plan for Scale—and Change

Pilot-scale labs rarely stand still. As your science evolves and your business pivots, your lab needs to keep pace—without requiring a full teardown every time a protocol or process changes. The smartest setups are built with both today’s needs and tomorrow’s uncertainties in mind.

Modular Equipment vs. Custom Systems

Modular systems have become a go-to for pilot plants and fast-moving startups. They’re designed for easy reconfiguration, expansion, or even relocation. Need to add a new unit operation or modify a chemical process? Modular casework, reactors, or workstations can be rearranged or upgraded without interrupting your production process.

This flexibility is especially helpful when transitioning from laboratory scale to larger-scale runs—or when evaluating the viability of new products before committing to a full-scale buildout.

Custom-built systems, on the other hand, can be tailored for highly specific operating parameters and formulations. If your process is stable and ready for commercial scale, these systems can improve throughput and efficiency. But they come with tradeoffs: higher upfront costs, longer integration time, and limited adaptability to future scale-up changes or optimization needs.

Scalable Workflows

Think beyond instruments and look at your entire workflow. How will process steps link together at full scale? Can you expand your reactor capacity, add redundancy, or integrate wastewater treatment as volumes increase?

Planning tips:

• Design utility layouts that support future equipment additions.
  
• Leave space for additional units (like a second bioreactor or TFF system).
  
• Build in buffer capacity to absorb variability in raw materials, output volume, or heat transfer needs.

Leverage Leasing to Reduce Sunk Costs and Support Future Pivots

Leasing isn’t just about spreading out costs—it’s a strategic way to build flexibility into your scale-up journey.

By leasing pilot-scale or large-scale production equipment, you can:

• Avoid locking in capital on equipment that may not fit your next process iteration.
  
• Align your infrastructure with actual demand rather than forecasted growth.
  
• Reduce risk during early feasibility testing or while finalizing your chemical engineering methodology.
  

Many providers offer leasing packages tailored for biotech and chemical startups, including maintenance, calibration, and flexible lease terms. These programs make it easier to scale processes across different stages—lab scale, pilot scale, and ultimately commercial production—without overcommitting.

Operator perspective: If your team had to change direction in six months—new product, new process, or new operating conditions—how quickly and cost-effectively could you adapt your setup? Leasing can be a safeguard against getting stuck with the wrong tools.

Budget Strategy: CapEx vs. OpEx Considerations

When it comes to outfitting your pilot-scale lab, how you budget for equipment can have a big impact on your cash flow, flexibility, and long-term growth. The choice between capital expenditures (CapEx) and operating expenses (OpEx) isn’t just accounting—it’s a strategic decision tied to scalability, process viability, and your startup’s ability to navigate different scales of production.

Understanding CapEx and OpEx

CapEx refers to buying equipment outright or investing in major infrastructure—like building out a pilot plant or purchasing large-scale processing systems. These costs are capitalized and depreciated over time.

OpEx covers ongoing costs like equipment leasing, service contracts, reagents, and utilities. These are expensed immediately and often provide more budgeting agility as you refine your operating parameters.

Why It Matters for Pilot-Scale Labs

CapEx may make sense when:

• You have strong reserves or access to low-cost financing.
  
• Your production process is stable, and equipment is unlikely to be replaced in the short term.
  
• You’re building toward full-scale commercial production in-house and want control over asset ownership.
  

OpEx, on the other hand, is often the better fit when:

• You’re still optimizing your chemical processes and need flexibility in your setup.
  
• Your business model depends on speed, adaptability, or frequent changes in formulations or production scope.
  
• You’re concerned about overcommitting before feasibility, variability, and operating conditions are fully known.
  

Leasing as a Strategic Middle Ground

Leasing lets you scale up operations without massive CapEx outlays—ideal for biotech and chemical startups navigating the transition from bench scale to pilot scale, and eventually to industrial scale.

It also:

• Reduces sunk costs on equipment you might outgrow.
  
• Makes it easier to match spending with evolving methodologies and process optimization efforts.
  
• Allows you to respond to new technologies and regulatory shifts without waiting for depreciation cycles to run out.
  

Real-world considerations:

• Cash flow: Smooths expenditures across project timelines, helping you focus capital on high-priority R&D or hiring.
  
• Facility planning: Lets you adapt infrastructure to meet changing needs—whether that’s installing a new heat exchanger or resizing for larger reactor volumes.
  
• Tax implications: CapEx offers depreciation; OpEx can be fully deducted—your finance team can help model what’s best for your situation.
  

Operator insight: Many scale-up teams use a hybrid approach—owning durable, low-risk equipment (like cold storage or basic utilities) and leasing tools tied to variable processes or evolving validation requirements. Flexibility is the name of the game when planning across different scales.

Final Tips for a Smoother Pilot Lab Buildout

Even with a strong plan, pilot-scale buildouts come with surprises. The smallest oversight—whether in your mathematical model, process design, or utility layout—can snowball into major delays. These tips can help you stay ahead of the curve.

1. Involve Facilities and Process Teams Early

Successful scale-up efforts hinge on aligning engineering, operations, and lab teams from the beginning. Your chemical engineering and facilities leads can flag floor plan risks, utility gaps, or overlooked flow rates long before equipment hits the dock.

2. Validate Utilities and Floorplan Before Delivery Day

Don’t assume your space is ready. Confirm every input—power, process water, drainage, HVAC—is sized and located correctly for each piece of equipment.

Walk the space with a tape measure. Account for equipment clearances, mass transfer limitations, and waste disposal routing. Misjudging these can derail validation or cause unnecessary downtime.

3. Consider a Phased Install to Minimize Operational Risk

Rather than installing everything at once, consider a phased rollout. Start with core systems, validate under controlled conditions, and scale gradually. This approach makes it easier to assess feasibility and catch problems before expanding into full-scale mode.

4. Build in Flexibility for Future Changes

Design with reconfiguration in mind. Modular benches, mobile reactors, and flexible utility lines make it easier to support new workflows, formulations, or chemical reactions down the road.

If you plan to scale process volumes or add capabilities like evaporation units or wastewater treatment systems, leave room—both physically and financially—for upgrades.

5. Document Everything—From Specs to Lessons Learned

Keep a living document that captures:

• Equipment specs and installation needs
  
• Utility requirements and operating parameters
  
• Lessons from pilot studies, failed runs, and optimization cycles
  

This record will support smoother onboarding, better provider negotiations, and faster adaptation if your production model shifts.

Final thought: No pilot lab is ever truly “done.” Whether you’re ramping toward commercial scale or adjusting to a new round of funding, the goal is to build a setup that lets you scale, optimize, and pivot with confidence—so your science can move forward without infrastructure getting in the way.