Purpose: The purpose of this paper is to analyse how collaborative/opportunistic behaviours within subsidised university-industry partnerships are influencing the design/implementation of strategic knowledge management practices in emerging economies. Design/methodology/approach: The proposed conceptual model was analysed with a retrospective multiple case study approach integrated by four subsidised entrepreneurial universities-industry partnerships of the Incentive Programme for Innovation from 2009 to 2014 in Mexico. Findings: Entrepreneurial universities and industrial organisations confirm insights about dual collaborative-opportunistic behaviour within subsidised partnerships. The main effects of behaviours represent an increment in the knowledge management costs during the monitoring stages. The ex ante collaboration agreement anticipated and protected intellectual capabilities. Research limitations/implications: This research contributes to the ongoing discussion about public administrations’ opportunistic behaviours in emerging economies (Tripsas et al., 1995), the effectiveness of the innovation and entrepreneurial programmes (Guerrero and Urbano, 2019b), and the link between dual behaviours (collaborative and opportunistic) and knowledge management practices (de Wit-de Vries et al., 2018). Practical implications: New questions emerged about the effectiveness of subsidies as new modes of knowledge generation among entrepreneurial universities and industrial organisations, as well as the need for implementing strategic knowledge management practices in the public administration. Social implications: For policymakers, the study presents insights about the effectiveness of public resources. Policymakers should understand challenges and re-define/re-incentivize the productive value chain as well as implement mechanisms to control opportunistic behaviours on potential subsidised firms. Originality/value: The paper contributes to the academic debate about how entrepreneurial universities and industrial organisations are strategically managing their knowledge when participating in subsidised partnerships in emerging economies.