For the time being, companies and organisations are being forced to compete in utterly complex and globalised environments, facing massive natural, economic, and technological challenges on a daily basis. Addressing these challenges would be impossible without a proper approach that helps them identify, measure, understand, and control the performance of their organisations. Lean principles and techniques rise as a solution. This paper justifies and proposes the use of lean principles and techniques to identify key performance indicators (KPIs) in project-based organisations based on their organisational and operational needs. The research focuses mainly on the identification and categorisation of KPIs through a qualitative approach, based on systematic literature review (SLR) of performance indicators, project management, and project success. As a case study, an analysis of relevant information of an R&D and innovation project-based organisation, such as quality manuals, a benchmarking process, internal studies, and surveys regarding what success means for different kinds of stakeholders and for the organisation itself was conducted. As a result, this research is of a high value for project-based organisations, especially those that are not apprised of how to correctly formulate a series of KPIs, or whose path to it is still not clear.