Previous studies on the effects of virtual and physical manipulatives have failed to consider the impact of prior knowledge on the efficacy of manipulatives. This study focuses on the learning of plane geometry in junior high schools, including the sum of interior angles in polygons, the sum of exterior angles in polygons, and the properties of parallel lines. This study adopted a quasi-experimental design of pre-test and post-tests with nonequivalent groups. The participants comprised four classes in the 8th grade. Students were randomly divided into two groups: the virtual manipulatives group and the physical manipulatives group. Two-way factorial analysis of covariance was adopted to compare the impact of manipulatives (virtual vs. physical) and prior knowledge (high vs. low) on learning outcomes and attitudes toward mathematics. Our results demonstrated that students with high prior knowledge using virtual manipulatives had better post-test performance than did the physical manipulatives group, and reported taking greater enjoyment in mathematics. These students also perceived the importance of mathematics more strongly than those with low prior knowledge. Students with high prior knowledge also presented stronger motivation to study mathematics and freedom from fear of the subject than those with low prior knowledge.