In the context of creating the European Research Area, many European universities are now engaged in different research activities including international research projects, which can make a valuable contribution to the development of an academic organization. Partnership of three higher education institutions from three countries was organized to implement LEARNIT research project: WSEI (University of Economics and Innovation, Poland), KVK (Klaipeda State College, Lithuania), and TSI (Transport and Telecommunication Institute, Latvia). The key project outcomes are supposed to be the properly equipped Learning Lab and software for mobile devices intended for enhancing the effectiveness of the learning process by stimulating students' concentration. LEARNIT is a complex multidimensional research project that involves people of different professions and positions: researchers, managers, teachers, IT specialists and students. Therefore, the management of LEARNIT is a complicated process that requires strong integration of various resources, as well as different pedagogical and managerial procedures. The aim of the paper is to address the main challenges faced by the LEARNIT management in the project implementation process, and to describe key focus areas of this project. The analysis provided in this paper is based on the academic literature review on the major educational and project management issues; it is also based on the author's experience as the project leader from Transport and Telecommunication Institute. The analysis performed in this paper allows the author to conclude that the implementation of a cross-disciplinary research project demands using the holistic approach to the management of heterogeneous organizational resources. The success of a cross-disciplinary research project is directly related to the accomplishment of a synergistic effect; the expected synergistic effect arises from strong cooperation between main functional domains of a university, so the project should be aligned with the appropriate management functions carried out in the agenda of functional area-specific strategies implementation. The author hopes that whatever lessons this analysis provides would be helpful to managers responsible for implementing a complex research project in a modern university.