This study analyzes the perception, development and improvement of the cognitive abilities of undergraduate students (of biochemistry and industrial chemistry) through the application of an inquiry methodology in the laboratory of analytical chemistry. The study was conducted during one semester. The instruments for data collection were a Test of Critical Thinking and a Questionnaire to determine the perception of the inquiry methodology and the traditional methodology, applied at the beginning and at the end of the semester. The results show an improvement in cognitive strategies and in the students' perception of the inquiry methodology. This is consistent with future job performance.