Background: Recent advances in technology and computer simulation have expanded the use of virtual manipulatives in engineering education. However, especially in disciplines in which tactile concepts (e.g., force) are included, it has been claimed that learning could be compromised by substituting physical materials with computer simulations. Purpose: This study examines the comparative effect of physical and virtual materials on students' conceptual understanding and motivation to learn structural concepts with manipulatives. Method: The study followed a between-subjects design involving 209 university students and seven instructors. We used a pretest/posttest quasi-experimental design with a purposely developed conceptual test to measure students' understanding of basic structural engineering concepts. Motivation and its components (attention, relevance, confidence, and satisfaction) were assessed with Keller's Instructional Materials Motivation Survey. Results: Our results revealed that the physical and virtual conditions were equally effective in promoting students' understanding of basic structural engineering concepts in a classroom setting. We also found that the students were more motivated to learn through the use of physical materials than with virtual ones. This difference was especially significant in the attention dimension. Finally, we found that male students showed more confidence than female students when using physical manipulatives but not when using virtual ones. Conclusions: The findings from this study associate the benefits of using physical materials with an increase in motivation rather than with superior learning gains. In particular, engineering educators seeking to enhance students' attention should consider adopting physical manipulatives in their classrooms, although they must be aware of the potential sex differences that could be caused by their use.