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. Lay Description: What is already known about this topic: Technology's role, particularly online collaboration tools, in enriching science education is undebatable (Donkin & Rasmussen, 2021; Rahmawati et al., 2022). Such tools have been theorized to bolster student learning outcomes, motivation, and engagement (Donnelly et al., 2013; Ekici, 2017; Khazanchi & Khazanchi, 2019). Yet, the empirical evidence validating their efficacy in science educational settings remains sparse. What this paper adds: This research delves into the influence of online collaboration tools on science learning outcomes among middle school learners. Data indicates that employing these digital tools substantially elevates student performance, as gauged by a science achievement test. Furthermore, students navigating through these online collaborative platforms recorded elevated levels of both engagement and motivation. The primary effectiveness of online collaboration tools stems from their ability to foster specific behaviours, such as increased communication frequency and structured task management, which can amplify learning and group collaboration through their facilitated structured interactions. Implications for practice and/or policy: This study's conclusions offer pivotal insights for educators, academic institutions, policy framers, and curriculum architects. Online collaborative platforms exhibit promise in amplifying student outcomes and engagement within the realm of science education. It is imperative to broaden this research scope to discern the tools' potential across varied educational environments and diverse student demographics. There is a compelling case for stakeholders, especially educators and policymakers, to contemplate incorporating these online tools into science pedagogy, aiming to magnify student learning experiences and engagement levels. [ABSTRACT FROM AUTHOR]