The main object of the research was to elucidate the difficulties related to the creation of the innovative learning environment as an indispensable component of the innovative pedagogy. In order to achieve the proposed objective, there was analyzed the existing innovative learning environment in higher education in the Republic of Moldova in terms of its four core elements: learners; educators; content; resources. The practical investigation was carried out in two universities: Moldova State University and the State Agrarian University of Moldova. As a result of the research, the difficulties related to the creation of an appropriate innovative learning environment were identified and the directions to remedy the identified problems were proposed. The research methodology included: analysis, synthesis, generalization, observation, interviewing, opinion survey, formulation of reasoning and conclusions. The investigation was carried out within the project: "Support of teaching innovation, Research development and Inter-university cooperation of SAUM and TSU (Moldova)" funded by the Ministry of Foreign Affairs of the Czech Republic, Czech Republic Development Cooperation, realized by the Czech University of Life Sciences Prague (grant decision number 7/2021/7).