The initial learning experience is a critical opportunity to support conceptual understanding of abstract STEM concepts. Although hands-on activities and physical three-dimensional models are beneficial, they are seldom utilized and are replaced increasingly by digital simulations and laboratory exercises presented on touchscreen tablet computers. The purpose of this study is to measure the effectiveness of different pedagogical strategies (physical model building, digital model building, or traditional paper worksheets) on short-term and long-term conceptual understanding of an abstract STEM concept. A sample of 161 9th-grade students in six in-tact science classes participated in the study. Conceptual understanding was measured using an objective quiz, a drawing, and a hand-written constructed response explanation. Conceptual understanding was measured immediately after intervention and again two months later. To account for potential covariates, spatial ability and attitudes to scientific inquiry were measured and a conceptual understanding pre-test was administered. For both immediate and delayed post-tests, there were no differences among the groups for the objective quiz measure. However, the physical model group outperformed the digital model and control groups in both the drawing and constructed response measures at both timepoints (p < 0.01). Spatial ability was a significant covariate for objective quiz and drawing measures. Attitudes were not significant throughout. These results suggest that, at the initial learning experience, hands-on manipulation of three-dimensional physical models better aids conceptual understanding in the short term and the long term when compared to two-dimensional touchscreen devices and that assessments should move beyond objective-based exams to accurately measure conceptual understanding.