The study focuses on the effects of four different affective variables, namely; well-being, perceived self-regulation, trust in the teacher, and alienation from school, on the academic achievement of middle school 6th grade students in the Science course. The participants of the study were composed of randomly selected 332 (156 girls, 176 boys) middle school 6th grade students in Ankara Turkey. The data were collected using the EPOCH Well-Being scale developed by Kern et al. (2015) and adapted to Turkish by Demirci and Eksi (2015); the Perceived Self-Regulation Scale developed by Aslan and Gelisli (2015); the Teacher Trust Scale developed by Adams and Forsyth (2009) and adapted into Turkish by Özer and Tül (2014); and the Student Alienation Scale developed by Sanberk (2003). Multiple regression analysis was used as a research method in the study. In order to determine the students' academic success in their Science classes, mean scores of the students' papers in four different written exams in the 1st and 2nd semesters of the 2018-2019 academic year were considered. In the study, initially, the correlations between the sub-dimensions of each affective variable and science academic achievement were examined. Models were created via stepwise regression analysis, starting from the sub-dimension that gave the highest correlation with science academic achievement. Sub-dimensions that did not contribute significantly to science academic achievement were removed from the model and its final shape was obtained. The results revealed that, the sub-dimension of EPOCH well-being was relatedness and the sub-dimension of perceived self-regulation being openness were significant predictors of academic success in the science course. These sub-dimensions explain 10% of academic achievement in science classes.