The purpose of this study is to identify the barriers of university and industry cooperation and to develop recommendations for the internal ecosystem of technology commercialization. The research method used is a survey of three categories of experts from 9 universities of Almaty (researchers, technology transfer managers, spin-off-owners). Despite the strong efforts of the government of Kazakhstan in building innovation infrastructure, there is a low level of innovation activity, less than 5% of university inventions are transferred into the industry. The results of the expert survey showed that the main barriers for cooperation between university and industry are: lack of resources to build university-industry links, lack of time due to high teaching load, poor qualification of technology transfer managers and lack of networking with industry. Based on the results of the expert survey, it is proposed to develop the ecosystem for the commercialization of university-based technologies, for which the following economic activities are important: human resources, financing, intellectual property management system, and intermediary infrastructure. The results of this study can be applied in developing the strategies and policies for universities, public research organizations, as well as for national R&D and higher education policies.