Background: Online collaboration tools have been identified as potentially effective means for enhancing student learning, motivation, and engagement in science education. However, their effectiveness in improving science education outcomes among middle school students remains uncertain. Objectives: The study aimed to investigate the impact of online collaboration tools on science education outcomes among middle school students, focusing on learning achievement, engagement, and motivation. Methods: A quasi-experimental design with a pretest-posttest control group was used in this study. A total of 60 eighth-grade middle school students were involved in the study, with both the experimental and control groups comprising 30 students each. The experimental group incorporated the use of digital collaboration platforms, including Asana, Slack, and Team Viewer, as instrumental components of group project execution and discussion in their science lessons. Conversely, the control group adhered to the current educational approach in Turkey, characterized by the employment of an inquiry-based learning strategy in their science instruction. Data was collected over eight weeks using a science achievement test, engagement scale, and science motivation scale. Results: The experimental group demonstrated significantly higher post-test scores compared to the control group, suggesting that online collaboration tools positively impacted science education outcomes. Additionally, survey data indicated high levels of engagement and motivation among the experimental group students when using the online collaboration tools. Conclusions: The findings support the notion that online collaboration tools can effectively enhance learning, motivation, and engagement in science education among middle school students. These results have significant implications for educators, educational institutions, policymakers, and curriculum developers. Further research is needed to examine the potential of these tools in various educational contexts and with different student populations. This will help broaden the understanding of how online collaboration tools can be integrated into diverse learning environments, potentially benefiting a larger number of students and further improving science education outcomes.