The hidden costs of over-customising an ERP system

Hidden costs
  • 5 minute read
  • 16 Jun 2026

Enterprise Resource Planning (ERP) systems are central to modern business operations, seamlessly connecting finance, supply chain, human resources and customer interactions into a unified digital framework. As companies embrace digital transformation, cloud migration, and AI-driven processes, deciding the extent of ERP customisation becomes a pivotal choice in any technology initiative. While customisation is often seen as a way to meet specific business needs, it frequently leads to hidden costs, technical debt, and long-term limitations that diminish the value of the initial investment. 

Organisations are now encouraged to rethink their ERP design approach, not by stifling innovation, but by ensuring each customisation is intentional, well-governed, and aligned with long-term goals. While customisations might offer short-term alignment with business preferences, their cumulative impact over the system’s lifecycle often outweighs the benefits.

Common challenges include:

Lack of standardisation

When departments demand varied customisations, the ERP loses its role as a central record. Process variations increase, reporting becomes fragmented, and the organisation ends up managing a patchwork of localised solutions instead of a cohesive enterprise platform.

lack of standardisation

High initial development costs

Custom code requires skilled developers, consultants, and architects. Costs extend beyond building to include detailed design, testing, documentation and knowledge transfer.

Initial development costs

Ongoing maintenance costs

Every customisation needs maintenance throughout the system’s lifecycle. Bug fixes, regulatory updates, and compatibility adjustments create a recurring cost base often underestimated in the original business case.

on going costs

Upgrade complexity

Each customisation must be retested, reworked, or rebuilt during upgrades, increasing costs, and delaying the adoption of new features. This complexity is compounded when customisations involve integrations with other solutions or applications, leading to compatibility issues when those systems are upgraded.

upgrade complexity

Longer release cycles

Testing customisations slows the deployment of new features, lengthens release cycles, and undermines the agility the ERP was meant to provide.

Longer release cycles

End-of-life risks

When platforms or components are deprecated, custom code becomes a liability. Migration projects become significantly more complex where heavy customisations have accumulated.

End of life risks

Inappropriate system controls

Customisations introduced without sufficient design can weaken the control environment, bypassing standard segregation of duties, audit trails and validation logic, increasing operational, financial, and compliance risk.

System controls

Tribal knowledge dependency

Critical processes often rely on a few individuals who understand the custom code. When they leave, the organisation is left vulnerable with limited capability to maintain the customisations.

Individual dependency

Failure to adapt

Customisations built today may not align with tomorrow’s strategy, limiting agility, and making it harder to adopt new operating models or integrate acquired entities.

Adapting

The right approach to ERP customisation

A disciplined approach doesn’t mean refusing to customise. It means ensuring every customisation is justified, governed, and architecturally sound, based on these principles:

Not every requirement needs a custom solution. Challenge every customisation request, leverage the leading practices that vendors such as SAP, Oracle and Microsoft have built into their platforms, and re-engineer business processes to fit the ERP rather than the other way round.

Create a cross-functional Customisation Review Board across IT, business, finance, and architecture with formal approvals, standardised templates, clear thresholds, C-level escalation for high-risk items, and a centralised registry.

Keep the ERP core clean and build extensions outside it. Use APIs and event-driven integration, adopt microservices and domain-driven design where appropriate, and ensure compliance with the enterprise reference architecture.

Justify each customisation through ROI, full TCO analysis, risk-adjusted NPV, sensitivity analysis, and benefits realisation tracking.

Align with ITIL, route production changes through a Change Advisory Board, adhere to release windows, and mandate rollback plans, blackout periods, and post-implementation reviews.

Track customisations through a roadmap, review them annually, retire them when standard functionality catches up, and allocate a dedicated refactoring budget.

Together, these principles shift customisation from a reactive response to a governed, strategic discipline that preserves agility, controls cost, and protects long-term value. A disciplined approach begins with a clear principle: configure first, customise only when it delivers genuine competitive advantage. This means distinguishing commodity processes from differentiating ones and aligning each decision with strategic objectives.

How can we help?

We support organisations at every stage of their ERP journey. Backed by our global Centre of Excellence, industry accelerators, and regulatory expertise, our services range from end-to-end implementation, cloud migration, post-go-live support, current system evaluation and support, customisation assessments, governance design, architectural advisory, and cybersecurity. Our goal is to help organisations build ERP systems that are ready to adapt and deliver lasting value, guided by the principle that the best customisation is often the one you didn’t need to build.

Our capabilities span the full enterprise technology stack, including:

  • Oracle Fusion ERP

  • Oracle Fusion Procurement

  • Oracle Fusion Supply Chain Management

  • Oracle Integration Cloud (OIC) 

  • Oracle Cloud Infrastructure (OCI)

  • Oracle Data Integrator

  • Oracle Business Intelligence

  • Dynamics 365 Finance & Supply Chain Management

  • Dynamics 365 Business Central

  • Microsoft Azure

  • Microsoft Power Platform 

  • Microsoft Power BI

  • Microsoft Copilot and AI Agents

  • Microsoft Fabric

  • Microsoft Purview 

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Andrew Schembri

Andrew Schembri

Digital Services Partner, PwC Malta

Tel: +356 7921 1355

Etienne Falzon

Etienne Falzon

Director, Digital Services, PwC Malta

Tel: +356 7973 6377

Ahmad  Khan

Ahmad Khan

Manager, Advisory, PwC Malta

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