The aim of this study is to investigate the effects of Project-Based Learning (PBL) and Flipped Classroom Model (FCM) supported by PBL on sixth grade students' academic achievement, retention of knowledge, and individual innovation competence. A quasi-experimental design with a pre-test and post-test control group was used in the study. While the PBL method was applied to the first experimental group, FCM-supported PBL was applied to the second experimental group. In the control group, teaching was carried out according to the science curriculum. The study was conducted with 80 sixth grade students from three classes during the 2021-2022 school year at a public middle school in Mugla, a province in Turkey. The Matter and Heat Achievement Test (MHAT) and the Individual Innovation Competence Scale (IICS) were used as pre- and post-test measurements. The results revealed that the students who participated in the PBL group and FCM-supported PBL achieved significantly higher post-test scores than those in the control group, indicating increased academic achievement. However, no significant difference was found between the groups in terms of individual innovation competence. It was also observed that the PBL group had significantly higher retention scores than the control group. Investigating the long-term effects of these instructional approaches across different subjects and grade levels would be beneficial.