The aim of the present study was to investigate the effect of a learning environment designed in accordance with Model-Based Teaching and Learning method on fourth grade students’ levels of understanding and mental model development regarding the definition, structures, functions, behaviors, mechanisms and forms of microorganisms. In the study, mixed method was adopted. The sample consisted of 6 students from a school located in a village of the central district of Kastamonu province. Data were collected by means of “Microorganisms Concept Test” and semi-structured interviews both before and after the teaching practices. Data from the concept test were analyzed with due consideration to the levels of understanding of the students. Descriptive analysis was employed for the analysis of the qualitative data. When the final interviews conducted both before and after the teaching practices were compared and contrasted, students’ overall levels of understanding were found to rise and within the scope of the study, it was seen that they reached a scientific model concerning microorganisms. ModelBased Teaching and Learning practices promoted students, in terms of mental models, to reach the scientific model about microorganisms. However, it was also seen that incomplete and alternative conceptions about the different aspects of microorganisms persisted in some students’ minds.