Beyond configuration: the centrality of the process in MES implementation

“Implementing a Manufacturing Execution System (MES) is not just about configuring software. It means digitizing complex and quality-critical GMP processes. Without a real understanding of the process, the issue is not an occasional mistake: it is a system-level risk.”

In the pharmaceutical sector, MES and digitalization are closely linked to data traceability and control. However, implementing an MES is not a straightforward IT activity; it represents the digital transformation of regulated production processes that are highly sensitive to quality. For this reason, process knowledge is not merely a useful extra;. It is a core requirement for the MES consultant.

What must an MES consultant understand about pharmaceutical manufacturing?

To work effectively, the consultant must understand the key phases of production at least at a structural level.

They must be able to interpret:

• Dispensing and weighing of raw materials

• Bulk manufacturing, from mixing through activities upstream of product release

• Primary and secondary packaging

• Materials, quality states, deviations, and reworks

• Electronic signatures, holds, locks, releases, and operational responsibilities

• Role-specific responsibilities across operators, supervisors, and QA

With this foundation, analysis workshops can use the right questions to identify critical issues before validation or go-live.

This is also where understanding the process becomes essential. In regulated manufacturing, the quality of the digital model depends on the quality of the process understanding behind it.

AS-IS vs TO-BE: when operational reality drives the MBR design

In MES design, the AS-IS approach works only if the digital model truly reflects how work happens in practice. If AS-IS remains anchored only to document logic, it becomes “paper on glass”: compliant in form but not verified in operational behavior. For example, activities that can be in parallel in real life might be modeled sequentially just for document clarity.

If the MES is not re-aligned to the real process, unnecessary constraints may be introduced, along with artificial waits and impacts on execution times.

In the TO-BE, analyzing the real process leads to a controlled remodeling of steps, preserving traceability and GMP requirements while aligning the digital flow with line operations. In this context, “replicating paper” means moving paper-based steps into a system without rethinking them in light of GMP intent. The result is often a platform that reflects module structure rather than the required quality controls creating unnecessary constraints, bottlenecks, low-value data, and less effective checks. This also increases Data Integrity risk.

Moreover, if the client team lacks process digitalization expertise the MES can be “configured correctly” without delivering the expected business-case value. Consulting is therefore critical to transform AS-IS into TO-BE using risk-based logic and to align mappings, responsibilities, system states, and registration criteria with real operations.

Compliance and Data Integrity: configure with risk in mind

Under GMP, each configuration decision can affect quality and compliance.

MES manages critical data, including process parameters, quality controls, electronic signatures, and audit trails. Therefore, principles such as ALCOA+ and related regulations (for example, EU GMP Annex 11 and 21 CFR Part 11) must be linked to process understanding.

Only then does it become clear where records, signatures, and additional controls are required, and how to handle deviations without weakening traceability.

If the consultant does not know the process, there is a tendency to add excessive controls that impact operations, or to add insufficient controls that create audit risk. Process knowledge enables a risk-based logic in which configuration follows the real criticality of the activities.

Real benefits of truly implementing MES

An MES is not an isolated system. Typically, it integrates with ERP for production orders and material management, with LIMS for analytical results, and with automation and serialization systems.

Understanding the process also means understanding the end-to-end flow, from order release through to batch release.

If the consulting team focuses only on technical interfaces, organizational misalignments can emerge: inconsistent material statuses, delays driven by laboratory turnaround times, or production holds caused by integration logic that is not aligned with operations.

A process view helps design integrations that truly support execution.

In this context, review by exception, controlled handling of cases that fall outside predefined rules, becomes fully achievable thanks to integration: when systems share consistent states and rules across the end-to-end process, exceptions are detected with the right context, assessed, and handled through dedicated workflows. Even in projects without integration, review by exception still provides structured governance of nonconforming situations: making exceptions traceable and addressed at the right time, reducing ambiguity, delays, and manual “after-the-fact” reconstructions

How does MES turn digitalization into continuous improvement?

An effective MES consultant does not simply “transfer” data into a system. They turn data into actionable evidence that helps QA assess the compliance impact and helps manufacturing and IT make changes sustainable over time. The consultant is a “translator”: they convert operational needs into configurations, regulatory requirements into digital controls, and technical constraints into practical solutions.

In regulated environments, the difference between a configuration provider and a high-value consultant lies in the ability to read the process, recognize its critical points, and propose choices consistent with business goals and the GMP context.

Strategic implications: from the MES project to governance continuity

When the MES is built on real process understanding, predictability increases, deviations decrease, and data for decision-making becomes more reliable.

To achieve this, the MES must operate as an operational asset, with clear responsibilities, control rules, change management, and decision continuity throughout the system lifecycle.

In this model, the consultant supports process modeling and helps define control choices. The Business Owner and the involved functions ensure ownership and alignment with plant objectives.

The fundamental condition for an effective MES implementation is to proceed together: the consultant and Operations must work with the same focus on the real process.

It also requires the willingness to revisit processes when necessary, supported by change leadership able to guide decisions and priorities. Otherwise, the MES may become limited to managing formal records rather than supporting daily execution.

Technology matters, but without a process that is jointly understood and governed, the MES value will not be consolidated.

Where should life sciences companies start?

• Map the real production process before configuring the MES.

• Test whether AS-IS documentation reflects operational reality.

• Identify where GMP controls, records, signatures, and audit trails are truly required.

• Design integrations around production flow, not only interface specifications.

• Define ownership, governance, and change processes before go-live.

• Treat the MES as a long-term operational asset, not a one-time IT project.