In the anatomical sciences, e-learning tools have become a critical component of teaching anatomy when physical space and cadaveric resources are limited. However, studies that use empirical evidence to compare their efficacy to visual-kinesthetic learning modalities are scarce. The study examined how a visual-kinesthetic experience, involving a physical skeleton, impacts learning when compared with virtual manipulation of a simple two-dimensional (2D) e-learning tool, A.D.A.M. Interactive Anatomy. Students from The University of Western Ontario, Canada (n = 77) participated in a dual-task study to: (1) investigate if a dual-task paradigm is an effective tool for measuring cognitive load across these different learning modalities; and (2) to assess the impact of knowledge recall and spatial ability when using them. Students were assessed using knowledge scores, Stroop task reaction times, and mental rotation test scores. Results demonstrated that the dual-task paradigm was not an effective tool for measuring cognitive load across different learning modalities with respect to kinesthetic learning. However, our study highlighted that handing physical specimens yielded major, positive impacts on performance that a simple commercial e-learning tool failed to deliver (P < 0.001). Furthermore, students with low spatial ability were significantly disadvantaged when they studied the bony joint and were tested on contralateral images (P = 0.046, R = 0.326). This suggests that, despite limbs being mirror images, students should be taught the anatomy of, as well as procedures on, both sides of the human body, enhancing the ability of all students, regardless of spatial ability, to take anatomical knowledge into the clinic and perform successfully.