6 Warning signs your PPM tool is holding you back and how to fix them?

Introduction

In a market flooded with Project Portfolio Management (PPM) tools, it is important to find one tool or a combination that fits your business needs, but does it end there? No, it doesn't. As portfolios continue to grow and evolve, so should the tools and processes around them.

Right from the evaluation of PPM tool capabilities and integration potential, to ensuring alignment with your project workflows, team structures, and governance models, the journey is anything but straightforward. What looks good on paper may fall short in practice if the tool doesn’t support your organization’s decision-making rhythms, reporting needs, or future scalability.

In this blog, we unpack some of the signs that indicate your current PPM may not be working for you.

6 Signs to change or upgrade your PPM tool

Whether you are managing a local functional level portfolio, or a global multi-therapy portfolio, your PPM tool should scale to match your future vision. Most of the times, the real problem lies in improper customization of the tool, or lack of proper alignment of the tool with the processes around it.

As time passes, even the most robust tools can quietly become misaligned as your portfolio grows in complexity and your processes and tool cannot catch up.

Here are 6 signs to watch out when your portfolio is growing.

1. Lack of visibility and transparency

In life sciences, where development timelines span years, costs reach billions, and go/no-go decisions hinge on granular data, lack of visibility isn’t just inconvenient—it’s risky. If stakeholders struggle to see the true status of projects, resource bottlenecks, or shifting priorities across the portfolio, it’s often because the PPM tool isn’t surfacing the right information in the right format.

This can result in

• Lack of progress visibility to the clinical project leads

• Resource managers cannot access real-time insights over-allocations across cross-functional teams.

• Finance and strategy teams operating with inconsistent data

• Limited visibility to the senior leadership for proactive decision-making

The fix:

• Integrate data across functions and systems

• Enable role-based dashboards

• Connect strategic governance to operational execution

• Adopt a layered approach: tools+analytics+services

2. Relying on manual processes

If your team is still exporting data from the PPM tool to create trackers, forecasts, or summaries in excel, they are building parallel processes outside the system.

In life sciences, clinical milestones are tied to regulatory submissions, resource planning needs to be done across multiple functional roles, and cost forecasting should be incorporated into scenario planning and PTRS-based risk adjustments. When spreadsheets are used for any of the above, it breaks traceability, auditability, and data integrity—which are non-negotiables in pharma.

The fix:

• Audit what is being done outside the tool and why

• Map critical decision areas (e.g., resource trade-offs, milestone projections, risk-adjusted value)

• Extend your current PPM tool with tailored integrations

3. Difficulty adapting to strategic change

In life sciences, strategic agility isn’t optional—it’s mission-critical.

Pipeline reprioritizations, licensing deals, market shifts, regulatory delays, and clinical data surprises are part of daily life. When your PPM tool can’t adapt quickly to these realities, it doesn’t just slow down operations—it weakens your strategic posture.

If your current tool requires

• Manual rework to update forecasts or resource allocations

• Weeks to reflect new prioritizations from governance

• Offline modeling of portfolio impacts

These can cause serious issues during some strategic triggers that require rapid adaptation. For example, businesses acquiring a biotech pipeline- Entire new projects and data sets need to be integrated rapidly.

The fix:

• Enable scenario modeling within the PPM environment

• Tie prioritization to strategic drivers

• Allow real-time, role-based replanning

• Connect strategic decisions to execute workflows

4. Data silos and integration issues

When systems cannot talk, people build manual work arounds, and that’s when errors, delays, and mismatches happen.

In life sciences, portfolio success depends on how accurate and real-time the data is flowing between clinical, regulatory, finance, and commercial teams. But if your PPM tool is not integrated well, it creates data silos, and decision-making blind spots.

For example,

• Clinical trial milestones are updated in the CTMS but not reflected in portfolio timelines,

• Finance forecasts in SAP does not align with resource assumptions in the PPM tool,

• Resource planning tools operate separately from program plans, creating over- or under-utilization

• The result? Reporting becomes reactive, portfolio insights become outdated, and governance decisions are made on partial or inconsistent data.

The fix:

• Identify and map critical data touchpoints

• Use APIs, data warehouses, or middleware for seamless flow

• Centralize reporting with a unified data layer

• Improve adoption by reducing complexity

5. Frequent project delays and missed timelines

In life sciences, R&D timelines stretch over years, and project delays and missed timelines can impact patient access, revenue realization, and consistent project overruns.

If projects across your portfolio are

• Slipping their milestones

• Missing regulatory submissions targets

• Requiring last-minute firefighting on resource or budget allocation

And the project teams have no visibility before this can happen, so it’s often not the science or the team—it’s a sign that the PPM tool is no longer providing the right foresight to plan and execute effectively.

The fix:

• Configure timeline logic to reflect real-world dependencies

• Add risk triggers and milestone health checks inside the tool

• Embed resource forecasting modules into the tool

• Activate portfolio-level impact tracking

6. Lack of reporting and analytics

If your PPM tool cannot generate the right reports, or it is bound to export raw data to just build custom views, then your PPM tool is slowing down decision making or is causing the team to rely on outdated decisions.

Common indicators are

• Complicated to compare budget vs actuals by function or program

• Reports lacking granularity and clarity

• Static portfolio views with no trend lines, variance tracking and drilldowns

Without timely, trusted insights, your team is stuck in reactive mode—reporting the past instead of steering the future. It is time to explore the reporting capabilities of your existing tool or evaluate the need to build an external reporting system.

The fix

• Design role-based dashboards for decision-makers

• Integrate real-time performance tracing

• Include trend analysis and historical views

• Layer predictive analytics for decisions

• Build Reporting Database and integrate data from PPM tool, financial tools

Conclusion

Adopting a PPM tool means countless hours of research, training and change management. Even if you notice one or many of these warning signs, you need not always replace the entire tool. Many times, with a few customizations and process fixes, portfolio management systems can be configured to support your growing portfolio needs.

i2e can helped global life sciences organizations fix and extend their PPM tool capabilities by

• Designing a maturity-based roadmap customized to your portfolio complexity

• Extending the current PPM tool with integrated analytics and dashboards

• Configuring milestone logic, risk signals, and resource forecasting inside your tool

• Automating reporting and scenario planning across portfolio layers