This study explores the effects of Metaverse technology on middle school learners’ academic performance and motivation in science subjects. Utilizing a quasi-experimental design, 33 students in the experimental group were exposed to the Metaverse for one semester, while 32 students in the control group continued with traditional teaching methods at School 148 in Riyadh. Data collection instruments included a validated science achievement test and a motivation scale. The results demonstrated that the nodes were statistically significantly improved in the experimental group, receiving an average post-test score of 73.1, as compared with the control group, receiving an average post-test score of 65.9 (t = 2.3, p < 0.05). The scores in motivation were also slightly higher in the experimental group, with a mean of 26.9, as compared with the control group, with a mean of 17.1 (t = 5.75, p < 0.05). For academic achievement and motivation, the effect sizes were quite high: fixed effect = 1.091; random effect equals 1.086. These results demonstrate the possibilities of Metaverse technology in revolutionizing the way students learn science. This technology could be a valuable tool for instruction in science classes to enhance performances and influence students’ attitudes positively towards enhanced learning environments in schools.