Simplicity wins: How Lean principles and smart automation can reshape pharma manufacturing

In pharmaceutical and especially advanced therapy manufacturing, the pressure to scale up, accelerate timelines, and cut costs has never been greater. In response, many organisations have turned to new digital systems, layers of oversight, and waves of automation, only to discover that performance hasn’t improved and that what they thought was the solution, now is the problem.

Teams are drowning in endless dashboards, redundant controls, and “initiative fatigue”. Yet, the manufacturers truly outperforming their peers share a defining trait: a ruthless commitment to simplicity, built on Lean principles and purposeful automation.

Lean thinking: A timeless framework for a changing industry

Lean manufacturing was born in the automotive industry, but its logic applies universally: value is defined by the customer, and anything that does not add value is waste. Lean is about doing more with less, and better.

In pharma, this means:

• Reducing non–value-added steps in production and documentation
• Streamlining approvals and batch record flow
• Minimising waiting times and unnecessary handoffs
• Building quality into the process, not inspecting for it afterward

However, applying Lean principles in a regulated environment demands nuance. Compliance requirements are real and essential; the challenge lies in distinguishing what’s required from what’s redundant.

The goal isn’t to strip out structure, but to build clarity, flow, and empowerment into every layer of the organisation. When done well, Lean manufacturing transforms complexity into visible, manageable systems that invite continuous improvement.

The pitfalls of overcomplication

In the past decade, the pharma and advanced therapy industries have been lured by digital transformation and automation at scale. But without a clear process foundation, these investments can become counterproductive, and in many cases become a money- and time-sink with no clear ROI.

Common symptoms of overcomplication include:

• Multiple systems tracking the same data in different formats
• Use of machines and software to force-feed media into your cell culture when it is proven obsolete
• Automation layered onto unstable or immature processes
• Local optimisation that damages overall throughput

The result is often more noise and less clarity.

Operators spend time feeding systems instead of improving them. Engineers chase data discrepancies instead of root causes. Quality teams drown in documentation while missing the real signals.

In advanced therapies, where biological variability is inherent, this complexity multiplies risk. Every deviation becomes an escalation. Every improvement requires a task force.

Lean principles offer a simple reminder, that the purpose of a process is to create value, not data. The purpose of a tool is to make people more capable, not more dependent.

Simplicity as a competitive advantage

Simplicity is not the absence of sophistication, it’s the essence of it. A well-designed process removes friction, clarifies accountability, and accelerates flow.

In Lean terms, simplicity strengthens the three critical flows of manufacturing:

1. Material flow – inputs move continuously without interruption or rework
2. Information flow – teams have immediate access to what matters most
3. Decision flow – issues are visible, and corrective actions are fast and empowered

A simple process is a visible process, and what’s visible can be improved, standardised, and ultimately automated.

Organisations that design for simplicity don’t just operate more efficiently, they adapt faster. They can scale without losing control, automate without overengineering, and innovate without chaos.

Smart automation: The right tool at the right time

Automation amplifies human potential, but only when applied at the right stage of maturity. Starting from Lean principles before automating, also called autonomation, prevents technology from magnifying inefficiency.

Four simple rules guide smart automation:

1. Simplify before you digitise. Remove waste and redundancy first.
2. Automate what’s stable. Don’t mechanise uncertainty.
3. Design for scalability. Favour modular, adaptable systems.
4. Keep humans in the loop. Even in high-tech environments, insight and visual control matter.

When automation builds on a simple foundation, it drives exponential gains. When it doesn’t, it just adds layers of cost and confusion.

Case study: Lean principles in cell manufacturing

Automation is being hailed in some corners as a panacea for cell therapy manufacturing, a space where commercial scale-up has been particularly challenging given the unique requirements of the new modality. A variety of automated solutions have been proffered with little concrete progress to show for them. Here may be the clearest example of the power of simplicity.

Instead of adding layers of complexity, better engineering can make the cell expansion step both straightforward and scalable. One robust approach uses a gas-permeable membrane, the boundary layer, to support high-density cell growth, enabling natural circulation to eliminate the need for complex perfusion loops or multi-step bioreactor systems. This creates a highly repeatable and consistent microenvironment from cell to cell and process to process. It’s a Lean design in action:

• Flow: Continuous gas exchange and nutrient delivery reduces interventions
• Built-in quality: Stable consistent microenvironment conditions lower variability and contamination risk
• Minimal waste: Less handling, fewer disposables, more efficiency

Leveraging the basic physics of the boundary layer, the microscopic point of contact between the cell surface and a fluid, demonstrates how simplicity doesn’t just make manufacturing easier, it makes it automatable. Once a process is stable, standard, and predictable, automation becomes straightforward and cost-effective.

Simplicity is the ultimate sophistication

Leaders often respond to challenges by adding: more systems, more reviews, more oversight. The intention is to ensure control, as scalability comes from control, but the outcome is often the opposite. Complexity breeds confusion, which breeds errors, which requires more control.

The most effective leaders in pharma manufacturing today are those who remove layers, not add them. They invest in clarity, trust, and capability, empowering teams to solve problems, rather than manage bureaucracy.

Implementing Lean principles is not a branding exercise; it’s a cultural one. It requires humility, focus, and a willingness to ask, What really adds value here? When simplicity becomes a leadership principle, everything else – quality , speed, and even innovation – flows naturally.

Pharma and advanced therapy manufacturing will only grow more complex in science, regulation, and global scale. But the solution will never be to add more layers of complexity, it will be to cut through them. Lean principles provide the compass. Simplicity provides the momentum. Smart automation provides the reach.

The future will not belong to those who build the most elaborate systems. It will belong to those who design the clearest ones, where every person, process, and technology works in flow. The lesson is simplicity is not the opposite of sophistication, it’s the path to it.

About the author

Ignacio Núñez is the chief operations officer at CellReady and a life sciences technical operations leader with extensive experience improving and scaling complex manufacturing systems. He specialises in Lean methodologies, operational excellence, and advanced therapy production, and has led major transformation programmes across biologics, cell and gene therapy, and other high-demand industries. His work focuses on driving process clarity, empowering teams, and enabling reliable, efficient manufacturing that expands patient access to next-generation therapies.