This study investigated the effect of varied digital presentation tools (PowerPoint and Prezi) on the learning performance of students. The research focus was to evaluate how different presentation technologies used by class instructors affect the knowledge acquisition of students. A quasi experimental pre- and post-test control group design was adopted to fulfill the research purpose. The educational experiment was completed within 4 weeks. The participants were 78 fifth-grade students from a public elementary school in Taiwan. Students from three classes were divided into three treatment groups: PowerPoint instruction, Prezi instruction, and traditional instruction. Two quizzes (formative evaluation) directly related to learning units were administered to assess the immediate learning outcomes of the students after class. A learning achievement test (summative evaluation) was developed to measure the basic geographical knowledge of the students in a social science class. Two weeks after the summative evaluation was completed, the same learning achievement test with different item numbers (delayed summative evaluation) was employed to assess the long-term learning effects of the students. The results showed that Prezi was a more effective instructional medium for knowledge acquisition compared with traditional instruction. PowerPoint demonstrated instructional effectiveness on only the long-term learning retention of the students compared with traditional instruction. However, no significant difference was observed among the three types of tests in Prezi and PowerPoint instruction. •Prezi was a more effective instructional medium for knowledge acquisition.•PowerPoint demonstrated instructional benefit on long-term learning retention.•No significant difference was observed between Prezi and PowerPoint instruction.