Enhancing students' conceptual understanding and improving their inquiry skills and motivation for learning science are the goals of science instruction in learning environments. The current study investigated how different inquiry-based learning environments (regular classroom and computer-based environments) affect middle school students' conceptual understanding of force and energy, inquiry skills, and motivation for learning science. A quasi-experimental pretest-posttest research design was used, with a total of 306 seventh-grade participants. A conceptual understanding test, an inquiry skills test, a motivation scale, and interviews were used to gather data. The findings revealed that the students in the computer-based learning environments showed significantly greater improvement than their counterparts in regular classroom environments in terms of conceptual understanding and inquiry skills. However, there was no meaningful difference in their motivation for learning science. Furthermore, the number of misconceptions about the topic of force and energy held by the students who learned in computer-based learning environments was relatively high. Possible reasons for the results including the advantages of instructional technologies, students' inquiry abilities, and factors affecting motivation are discussed.