In this series of blog posts, Lynette Nazabal, Client Solutions Executive, explores the strategic decisions you need to make when thinking about your Manufacturing Execution System (MES), the changing landscape of MES technologies, the questions you should ask, and how you should approach your MES vendor selection and implementation to maximize your investment decision. It’s time to think about your MES … Are you ready?  

Have you made a strategic business decision to implement a Manufacturing Execution System (MES) as part of your enterprise landscape and to complement your digital supply chain? If so, you might be thinking, “How do I execute an MES vendor selection that will provide the most visibility into the capabilities of all the technologies within the market?” or “How do I select a software partner that will support my business needs as they grow and evolve?”  

MES vendor selection requires careful consideration of how the solution will fit into your existing technology landscape and support your long-term business objectives. Taking time to establish your requirements and evaluate deployment options, including cloud vs. on-premise solutions, can help you make a more informed investment decision.

Below, we outline seven key considerations for an MES vendor selection:

MES Vendor Selection Considerations

Below, we outline key considerations for an MES vendor selection: 

1. Understand How MES Fits Within the Digital Supply Chain 

A digital supply chain can be complex and requires careful planning to ensure that the path for data integration is robust and compliant. MES plays an important role in capturing manufacturing execution data and equipment status, while supporting visibility into inventory movements. Understanding what data MES will receive and distribute to other systems is essential to define business requirements for your vendor selection phase. 

Having a digital supply chain roadmap that is inclusive of all enterprise and manufacturing systems will aid in identifying the role MES will play and the data flow between systems. It will also help you determine the right time and phasing of your MES implementation, as key data elements from certain systems (e.g., ERP) will allow for a much more unified and streamlined integration.   

2. Establish Business Requirements  

Understanding the business requirements for MES will help you make the most of your vendor selection. Evaluating the functionality and the offerings of each software vendor against your organization’s business needs can help determine the right MES for your company. For instance, you may not intend to interface with a LIMS system in the first phase, but you want to ensure it has the capability to do so when the time is right. How the software connects to other supporting systems, as well as network capabilities, should also be a key factor.  

In addition, ensure the software meets all Part 11 / Annex 11 Compliance requirements as well as provides dedicated system administrator privileges. Establishing comprehensive requirements before beginning an MES vendor selection can help ensure the solution supports your business processes today while accommodating future needs.

3. Cloud vs. On-Premise: Pros & Cons

In 2026, as the industry largely transitions from on-premise to software as a service (SaaS), cloud-based solutions (primarily with AWS or Azure), your organization needs to evaluate the two deployment models. Your organization should assess the models based on scalability, security, integration requirements, cost, and internal IT/OT capabilities. Cloud MES offers faster deployment, easier scalability, more timely updates, and stronger disaster recovery options through redundancy and geographic failover. On-premise MES provides greater infrastructure control, in addition to accommodating facilities with strict security, latency, connectivity, or legacy-system necessities.

For deployment of Cloud MES, your organization should first assess vendor backup, recovery, failover, data replication, and recovery time/recovery point (RTO/RPO) capabilities to ensure manufacturing operations can recover quickly in cases of disruptions.

4. AI Capabilities & Roadmap 

As AI capabilities continue to evolve, organizations should evaluate both the functionality available today and each vendor’s roadmap for future development. Focus on practical manufacturing use cases and how AI capabilities integrate with operational data. AI governance and human oversight should also be considered, particularly in regulated manufacturing environments. Organizations should also understand the complexity of integrating and adopting new AI capabilities, especially as their MES environment evolves.

5. Keep Support in Mind

The journey to achieve an optimal MES implementation can be lengthy and may take several phases depending on the scope. As your implementation progresses, the need for system support for the current state as well as future phases is important. System stability, performance, and security must be maintained as you implement new functionality and as the end user population expands.

Additionally, a strong support model must match your production activities in the event of a critical issue. It’s key to find a software vendor that provides the right level of support for your system and for your needs as part of the overall software package. Often, post-Go Live support and operational support fall short once a project is completed, as many life sciences companies don’t usually have internal teams in place to support these types of applications. MES software support and maintenance is a critical part of implementation and should be evaluated during the Request for Proposal (RFP) process.

6. Develop Strong RFP Guidance & Evaluation 

A Request for Proposal (RFP) should be a lot like shopping for a new house or a new car. You should understand your needs and business requirements prior to executing a vendor selection. Organizations should also understand how MES is going to sit within the enterprise landscape and what infrastructure capabilities will be needed to support system implementation. Providing detailed information and solid RFP documentation to the vendors to be evaluated can quickly determine what solutions may fit your business needs versus others that do not have certain capabilities.

While many vendors can claim to do just about anything, it’s important for the vendors to define whether they can provide most of your business requirements with out-of-the-box functionality versus a customized solution. The more customization, the more costly a solution can become. Taking the time to be thoughtful and organized with an RFP can provide a clear line of sight to the best MES solutions for your organization. Additionally, many MES vendors are the main source of implementation and support resources. MES vendor professional services organizations are a critical dimension of the RFP that need to be included and evaluated.

As you move forward with a MES vendor selection, consider the need and the cost to build capabilities internally or outsource to additional third parties, additionally evaluating if you should buy integration services from the vendor.  Vendor demonstrations based on your business requirements and current manufacturing processes can also provide valuable insights into how your business requirements translate into MES and confident the vendor understands your current needs.

7. Ask for Relevant Business Cases and References  

In the current landscape of technology providers in 2026, understanding a vendor’s capabilities and service offerings isn’t the only way to determine if a vendor is right for you. Demonstrating good customer relationships, as well as relevant business cases to support their expertise, should be an area of evaluation included in the vendor selection. An established MES provider should be able to supply equitable references to match your business, implementation approach, and manufacturing processes. In addition, relevant business cases will quickly establish whether a vendor has the expertise to understand your business processes and can support you as a long-term partner.

Selecting the Right MES for Today and Tomorrow 

Taking time to pick the right MES software can be a complex process, but the benefits of selecting the right MES and partner can accelerate the return on investment and provide operational efficiencies quickly to your organization. As the global MES market continues to grow – with a projection to reach $43 billion by 2030 – now is the time for your organization to start thinking about how to maximize your investment. 

If you are looking for a partner to assist with your MES vendor selection, Clarkston can help. 

Contributions from Spencer Simco

AI-assisted: A human led the content and final approval of this piece, with AI used to support ideation, drafting, editing, summarization, or repurposing.