ABSTRACT Background In Mexico, the undergraduate curriculum in biological, biomedical and related sciences only gives hands-on experience in 2D cell culture due to its low cost and ease of implementation. These traditional lecture-based cell culture courses are often limited to routine learning methods and fail to demonstrate alternative culture strategies that would be needed to realistically mimic the processes occurring within the human body and be used to solve relevant medical problems. The use of 3D cell culture, on the other hand, makes it possible to recreate a microenvironment similar to that of living tissue, which is extremely useful for physicochemical studies. Moreover, the incorporation of problem-based learning (PBL) techniques to teach 3D cell culture has the potential to greatly enhance student learning. Purpose The objective of the work herein was to evaluate the success of implementing a 3D cell culture technique using the PBL method of teaching. Sample In this pilot study, eight students attended a traditionally structured cell culture course to learn cell culture techniques (control group), and six students were taught using a PBL model. Design and methods The activities were carried out either with the guidance of an instructor (traditional learning) or through an autonomous search for information (PBL).3D cell culture and scaffold printing exercises were incorporated into the course schedule, fostering in our students the ability to solve real world problems within a team. Results With the PBL teaching method, students displayed a slight tendency to better interpret and discuss their results (P = 0.436). Conclusion This pilot study highlights the usefulness of self-learning through a PBL system and warrants larger-scale research to better examine the potential benefits of incorporating a PBL strategy for teaching 3D cell culture in undergraduate biotechnology engineering laboratories.