Purpose: Little is known about how subsidies enhance both collaborative and opportunistic behaviours within subsidized industry–university partnerships, and how partners' behaviours influence the intellectual capital dynamics within subsidized industry–university. Based on these theoretical foundations, this study expects to understand intellectual capital’s (IC's) contribution as a dynamic or systemic process (inputs?outputs?outcomes) within subsided university–industry partnerships. Especially to contribute to these ongoing academic debates, this paper analyses how collaborative and opportunistic behaviours within industry–university partnerships influence the intellectual capital dynamics (inputs, outputs and outcomes) of the subsidized projects. Design/methodology/approach: By combining two sources of information about 683 Mexican subsidized industry–university partnerships from 2009 to 2016, this study adopted the structural equation modelling (SEM) to analyse the effect of collaborative vs opportunistic behaviours in intellectual capital dynamics within subsidized projects. Findings: Our results show three tendencies about the bright/dark side of subsidies within the Mexican industry–university partnerships. The first tendency shows how collaborative behaviours positively influence intellectual capital dynamics within subsidized industry–university partnerships. The second tendency shows how opportunistic behaviours influence intellectual capital impacts (performance) and return to society (job creation). The third tendency shows how initial inputs of subsidized projects generate some expected socio-economic returns that pursued the subsidies (mediation effect of intellectual capital outputs). Research limitations/implications: This research has three limitations that provide a future research agenda. The main limitations were associated with our sources of information. The first limitation, we did not match subsidized partnerships (focus group) and non-subsidized partnerships (control group). A qualitative analysis should help understand the effect of subsidies on intellectual capital and partnerships' behaviours. The second limitation, our measures of collaborative/opportunistic behaviours as well as intellectual capital dynamics should be improved by balancing traditional and new metrics in future research. The third limitation is that in emerging economies, the quality of institutions could influence the submission/selection of subsidies and generate negative externalities. Future research should control by geographical dispersion and co-location of subsidies. Practical implications: For enterprise managers, this study offers insights into IC dynamics and behaviours within subsidized industry–university partnerships. The bright side of collaboration behaviours is related to IC's positive impacts on performance and socio-economic returns. The dark side is the IC appropriation behind opportunistic behaviours. Enterprise managers should recognize the relevance of IC management to capture value and reduce costs associated with opportunistic behaviours. For the university community, this study offers potential trends adopted by industry–university partnerships to reinforce universities' innovative transformation processes. Specifically, these trends are related to the legitimization of the university's role in society and contribution to regional development through industry–university partnerships' outcomes. Therefore, university managers should recognize the IC benefits/challenges behind industry–university partnerships. Social implications: For policymakers, the study indirectly shows the role of subsidies for generating/reinforcing intellectual capital outcomes within subsidized industry–university partnerships. The bright side allows evaluating the cost-benefit of this government intervention and the returns to priority industries. The dark side allows for understanding the need for implementing mechanisms to control opportunistic behaviours within subsidized partnerships. Accordingly, policymakers should understand the IC opportunity-costs related to industry–university partnerships for achieving the subsidies' aims. Originality/value: This study contributes to three ongoing academic debates in innovation and management fields. The first debate about how intellectual capital dynamic is stimulated and transferred through the collaborative behaviour within industry–university partnerships in emerging economies. The second debate is about the “dark side” of partnerships stimulated by public programmes in emerging economies. The third debate is about the effectiveness of subsidies on intellectual capital activities/outcomes.