Traditional lecture-based approaches have long been the cornerstone of undergraduate education; however, the paradigm is shifting towards more interactive and engaging methodologies. Flipped-classroom, online tools, gamification are only some of the recommended approaches. Thus, recognizing the transformative impact of collaborative learning, this article explores the introduction of group work via team projects in undergraduate microbiology courses as an innovative pedagogical strategy. Furthermore, a new concept of allowing students to select the specific topic from a predefined field, ensures the need to perform literature research and brainstorming during the course. As part of the activity, the students need to set-up their individual experimental plan. No formal instructions are provided on what work must be done. The selected techniques are subsequently validated in laboratory experiments and presented as a research project. As a result, after the course “Basics in Microbiology” undergraduate students have obtained skills not only in preparation of a scientific work (as precursor for Bachelors thesis), but also in teamwork, own task set up, and collaboration just within 13 weeks of study.