Significant changes are happening daily at all levels of society. Profit-based operations are faced with challenges posed by new events, but this is even more so in the case of non-profit organizations and institutions. The changes in the academic community as a consequence of the Bologna process having been introduced into teaching and overall functioning of the academia have brought about both positive and negative results. The opposition to the implementation of the new system into higher education has been caught in the gap between the old education system which still operates in practice and the necessity to implement new programmes in higher education teaching. The supporters of the traditional higher education system rightfully object that the process might become watered down, and that the European education system is not sufficiently harmonized. The Bologna process has introduced direct and indirect changes in the structure of the teaching process, as well as in new professions, such as "knowledge managers", who conduct formal and structural changes of the academic community. "Knowledge time", "knowledge industry" and the like require also a certain freedom in knowledge management. With the organizational changes the new "knowledge manager" receives additional tasks of being a real "leader" in restructuring the existing traditional organizations. Structural changes imply changes of values, i.e. changes in the way how business and teaching processes are evaluated. The realization of the Bologna process involves: emphasizing quality at all organizational levels of an academic community respect for individual creativity (students and teaching staff) and appreciation of individual contributions valuing individual efforts in class, home assignments and intellectual work devising a new assessment system, etc. New programmes in business and teaching processes are more or less successful in following the continuous transformation and autonomy of higher education institutions. However, the assessment of current organizational changes requires permanent adaptation of the current situation to new development trends.