The Triple Helix model of innovation is unquestionably the most discussed model for innovation in both developed and developing countries. This model advocates reinforcement of the cooperation between the university, business and government. The world is changing rapidly; consequently, this innovation model is mutating by taking different forms of interactions and collaborating under various conditions, posing various challenges and barriers toward three agents’ interactions. There have been many studies on three helices relationships type, three actors` interaction cases and main challenges. However, few studies concerning the Triple Helix model examined the managerial challenges in academia in realizing the Triple Helix Model and University-Industry linkages. A significant role is imposed on universities as the primary source of new knowledge, ideas, creativity and innovation. To push forward the strengthening of the university-industry collaborations within the Triple Helix model in universities of Kazakhstan, we aimed to define the main managerial challenges and barriers in other developing countries in this model realization. As a result, the systematic literature review displayed many challenging aspects in the universities’ micro-level management and the main difficulties of university-industry collaborations. Key words: triple helix, university-industry collaborations, managerial issues.