The study explores the perceptions of the micro-credentials software ecosystem (MC-SECO) by higher education institutions (HEIs). Through a discrete choice experiment, we investigate how various dimensions of MC-SECOs influence decision-making processes within HEIs. We aim to understand the factors that facilitate or hinder MC-SECO implementation. Our research highlights the importance of collaboration, risk management, trust, sharing, and transparency in developing a cooperative and efficient ecosystem. Collaboration aiming at enhancing sensing and shaping opportunities and threats, seizing an opportunity, and reconfiguring the resource base (i.e., dynamic capabilities provided by the ecosystem) is crucial for decision-making. In contrast, the willingness to share physical resources is seen as an obstacle in the implementation process. Risk-avoidance strategies dominate HEIs’ decision-making. By investigating the preferences and reasons for the resistance of HEIs regarding MC-SECO implementation, this research contributes to the understanding of digital transformation in education, emphasising the need for ecosystems that support dynamic capabilities, openness, and innovation.