As a rule, flagship universities consider forming the core of the regional innovation ecosystem to be one of their main strategic goals. Achieving this goal involves not only creating an innovative infrastructure, attracting partners, but also developing social capital and innovative culture (the «soft» component of the ecosystem). The article studies flagship universities’ activities on the latter problem. The theoretical basis of the study is D. Douglas’s concept of flagship universities. The research methodology is a qualitative analysis of strategic planning documents and flagship universities’ official sites. The study showed that almost all the flagship universities aim at becoming the core of the regional innovation ecosystem. Insufficient attention is paid, however, to developing innovative culture and social capital. A number of universities do not set this task; nor do they target culture change in favour of ecosystem-friendly values. In almost all the universities studied, there is a shortage of specific managerial actions on influencing cultural values. The social capital is also underdeveloped, which can significantly impede the implementation of joint projects. The research might have certain limitations due to using only open access materials from the first-wave flagship universities. At the next stage of their development (after 2020), they should specify the goals and activities for developing innovative culture and social capital, as well as their benchmarks. Otherwise, the «hard» component of the ecosystem would not function. The results of the work may be of use for university leaders and their partners who are interested in the balanced development of flagship universities as ecosystem nuclei.