Promising results from the use of problem-based learning (PBL) as a teaching method in medical programs have encouraged many institutions to incorporate PBL into their curricula. This study investigates how applying hybrid-PBL (H-PBL) in a microbiology laboratory impacts students' higher-order thinking as compared to applying a lecture-based pedagogy. The experimental design compared the learning outcomes of two groups of students: the control group and the H-PBL group, for whom PBL cases comprised 30% of the curriculum. Both groups were taught basic skills for the microbiology lab by the same instructor. Using the traditional teaching style for the control group, the instructor offered each student what they needed for their experiments. The H-PBL group practiced experimental design, data analysis, theory proposal, and created research questions by using six study cases that were closely linked to the area of study. The outcome was measured using a pre- and post- assessment consisting of 24 questions that was designed by following Bloom's taxonomy of learning levels. A one-way ANOVA was used to analyze the data. The results showed that for the first three levels of Bloom's taxonomy— knowledge, comprehension, and application—there were no statistically significant differences between the H-PBL and control group gain scores as determined by a one-way ANOVA. For the knowledge level, f (1, 78) = .232, and p = .632; for the comprehension level, f (1, 78) = .004, and p = .951; and for the application level f (1, 78) =. 028, and p =.863. On the other hand, the gain scores for the three higher levels—analysis, evaluation, and creativity—improved for the H-PBL group. The analysis level showed statistically significant differences, with f (1, 78) = 4.012, and p = .049. Also, there were statistically significant differences in students' performance at the evaluation level, with f (1, 78) = 11.495, and p = .001, and the creativity level, with f (1,78 ) = 23.432, and p = .000. In conclusion, the study results supported the value of incorporating hybrid problem-based learning (H-PBL) into the traditional microbiology laboratory curriculum.