Despite critical thinking supporting a deeper understanding of the scientific process, university activities prioritize lower cognitive processes, such as remembering skills. Also, it is unclear whether gender biases in interest toward science exist in university science degrees. These hinder students from achieving their goals effectively since students’ test scores and motivation improve with project-based learning. The main goal of this study is to examine the influence of active methodology based on research project-based learning (RPBL) on students’ overall perception and its variation across gender groups in relation to the acquisition of higher-order cognitive skills. The RPBL activity will consist of a straightforward microbial ecology project in which the students will use conventional and affordable lab equipment. The project will address all higher-order thinking skills levels included in Bloom’s taxonomy. We evaluated students’ perception of their learning outcomes on lab and cognitive skills, including the effect of gender, using two online surveys we passed before and after the RPBL activity. The results displayed that the students’ opinion regarding the project was decidedly favorable. Most of the students view the potential effort required for these activities positively, as it pertains to the subject matter and enhances their learning. However, the gender differences that were observed prior to the project’s implementation disappeared once the activity was carried out. Female students lacked confidence in their statistical skills while they had high confidence in their laboratory skills compared to male students. After attending our RPBL activity, female students gained confidence in statistics, and male students gained confidence in laboratory skills. This project reveals that a straightforward and affordable RPBL activity, which would not suppose a substantial additional workload for university lecturers, holds the potential to serve as a valuable tool to eliminate gender segregation, enhancing students’ academic self-concept, and improving their prospects for success. Additionally, it emphasizes higher cognitive skills, particularly the critical thinking skills that are essential within the university environment.

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