Concept mapping methodology is a way of representing knowledge described as a useful tool in medical education. It was introduced in the pathophysiology curricular unit at NOVA Medical School in 2002, within an ongoing experience of problem-based learning. Our goal is to present a comparison between the students' opinions and performances in two academic years, 2017-18 and 2018-19, to evaluate the effects of pedagogical changes in the concept mapping methodology, applied in the last year, which is also described in detail. Our convenience samples were composed by 224 students in 2017-2018 and by 216 students in 2018-2019. The analysis used the students' responses to the yearly institutional questionnaire on the quality of teaching and to a specific questionnaire applied to evaluate the tutorial sessions of 2018-19. Both were anonymous, and the response rate was above 50%. A comparison was also made between the continuous assessment during the tutorial sessions, expressed as a final cumulative score, and the results of an obligatory multiple-choice final test. The students considered the introduced pedagogical changes useful in their different components, such as identification of core concepts, construction of mini-maps, and their inclusion in final global maps. The better performance of the tutors, signaled by the students in 2018-19, was probably due to the preparatory pedagogical sessions.