Complex system upgrades rarely fail all at once. They unravel quietly as dependencies stack, ownership blurs and risk compounds. For this biotech organization, a multi-vendor MES and ERP initiative reached that inflection point after an acquisition left critical gaps in planning, architecture and governance. With regulatory operations at stake and up to $500K in ERP costs on the line, leadership needed more than urgency; they needed control. MustardSeed was engaged to help the organization surface the real work, align stakeholders and guide the program back to a disciplined, executable path forward.

The Challenge: A Critical System Upgrade Falling Behind With Real Financial Risk

One of the biotech organization’s manufacturing facilities (an acquired site supporting highly regulated production) was running on a Manufacturing Execution System (MES) that had been out of support for more than three years. This created a hard dependency: the broader NetSuite ERP rollout could not proceed until the MES upgrade was complete.

The upgrade effort began nearly a year earlier with an original target of July 2025. By August, however, progress had stalled:

• There was no active project manager
• No reliable, end-to-end project schedule existed
• Much of the remaining work had not been fully identified or sequenced
• Teams across IT, development, QA, infrastructure and vendors were misaligned
• Issues routinely lingered without ownership or resolution
• Institutional knowledge had been lost following the acquisition

Leadership pressure increased quickly. A September launch was requested, but without a clear plan or aligned architecture, the date was not achievable.

When the September milestone was missed, the organization made a deliberate decision to extend its existing ERP system for six months at a cost of $200,000. While not the preferred path, this created the time needed to stabilize the MES upgrade and better align it with the ERP roadmap. A new April deadline remains in place, with an additional $300,000 renewal risk if readiness is not achieved.

At this point, the challenge was no longer speed alone; it was control. The organization needed clarity on what work remained, where risks existed, and how to move forward with discipline.

MustardSeed was engaged to help the team regain structure, align stakeholders, and guide the program toward a realistic and executable path.

The Approach: Re-Establishing Clarity, Structure and Disciplined Execution

MustardSeed’s role was not to replace the team, but to guide it through a reset, bringing structure where it was missing and helping the organization see the full scope of work required to move forward.

1. Reconstructing the Plan and Making the Remaining Work Visible

When MustardSeed assumed responsibility in August, there was no usable project plan. The schedule had to be rebuilt using the original Statement of Work and what could be validated from prior activity.

As the plan was reconstructed, several critical requirements surfaced: work that was necessary for delivery but had never been formally planned, designed or owned.

Key gaps identified included:

MES–ERP Integration & File Transfer

• An SFTP server required for file transfers between MES and ERP had not been designed or planned
• No decision existed on whether the SFTP server should remain on-premises or move to the cloud
• More than 2 million legacy files required cleanup
• Existing ERP system integration worked only in production; no QA integration existed
• Existing ERP system QA access had to be confirmed and enabled
• Additional third-party vendor support was required but had not been scoped

Network & End-User Readiness

• New network tunnels were required between the facility and Azure
• Approximately 65 manufacturing floor computers had not been validated for browser compatibility

Reporting & Compliance

• No design existed for generating the Electronic Device History Record (eDHR)
• No defined approach existed to rebuild eDHR reporting in Azure

Resiliency

• System failover and recovery had not been designed

Surfacing this work clarified why progress had stalled and provided a factual basis for decision-making.

2. Organizing the Program Into Clear Workstreams

Once the remaining scope was visible, MustardSeed helped reorganize the program into a structured delivery model with clear ownership:

• Architecture & Development: 11 workstreams with 13 detailed sub-streams
• QA Environment Activities: 2 workstreams with 15 sub-streams
• Production Readiness: 2 workstreams
• Go-Live and Post Go-Live: Managed as a unified execution package

This structure created a shared understanding of responsibilities, dependencies and sequencing across teams.

3. Improving Issue Resolution Through Structured Collaboration

To move away from stalled email threads and unclear escalation, MustardSeed helped establish a cadence of structured working sessions and real-time problem solving.

As a result:

• Issues were typically flushed out within 2–4 hours (rather than days)
• 12 issues and risks were mitigated
• 10 additional risks were formally identified and actioned
• Some issues were resolved in under a week
• More complex issues required 4–6 weeks, largely due to third-party environment constraints

This approach did not reduce the amount of work required. Instead, it increased urgency, accountability and clarity around how issues were addressed.

4. Guiding a Highly Fragmented Team Environment

Only two internal resources were involved consistently from start to finish. Many contributors were third-party consultants focused on narrow scope areas, which made end-to-end coordination challenging.

MustardSeed served as a guiding presence across the program by:

• Helping clarify roles and expectations
• Keeping workstreams aligned
• Ensuring risks were surfaced early
• Supporting consistent communication across teams
• Maintaining momentum during periods of uncertainty

From August through mid-December, the team met multiple times per week to coordinate progress, resolve issues and keep work moving forward.

The Outcome: A Stabilized Program With a Clear Path Forward

The engagement delivered an essential outcome: a program that had been opaque and fragmented was stabilized, aligned, and made executable.

Over the course of the engagement, the following conditions were established:

• The architecture and target design were aligned and agreed upon
• Remaining work and dependencies became fully visible
• Ownership was established across more than 20 workstreams
• Financial risk was clearly understood and actively managed
• Progress shifted from reactive firefighting to day-by-day readiness management

As a result, the organization moved from uncertainty to control, creating the conditions needed to move forward with confidence toward the next milestone.

Strategic Takeaway: Strong Project Leadership Creates Stability Before Speed

This engagement reinforces a simple truth: complex system upgrades don’t fail because teams lack effort; they fail when complexity goes unmanaged.

By guiding the organization through a structured reset (surfacing hidden work, aligning architecture, and reinforcing disciplined execution), MustardSeed helped the team regain control of a high-risk, multi-vendor MES and ERP initiative.

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