The aim of this study is to investigate the effect of engineering design-based Algodoo activities used in "Force and Motion" unit at 6th grade on students' design skills, academic achievement, and retention of learning. Designed as a pre-test and post-test quasi-experimental control group design, this research was conducted with 50 students (25 students in control group and 25 students in experimental group) from middle socioeconomic class attending a state middle school in Istanbul. In the experimental group, the lessons were taught according to engineering design-based Algodoo activities developed by the researchers, while in the control group the lessons were taught based on the curriculum following the science textbook. The data collection tools included an achievement test on force and motion, worksheets, video recordings and researcher notes. Independent samples t-test was used in the analysis of the data. Moreover, "Engineering Design Process Evaluation Rubric" was used in order to assess the changes in the design skills of the students in the experimental group. As a result of the research, it was found that engineering design-based Algodoo activities used in the "Force and Motion" unit contributed to the increase in students' academic achievement. In addition, it was understood that students made progress in the "identifying the problem or need", "developing possible solutions", "constructing the prototype", "testing and evaluating solution(s)" and "presenting the solution(s)" stages of the engineering design process.