Current studies reveal that meta-level variables are very important in learning; however, little research has been devoted to the role of metaconceptual and meta-affective variables on student achievement. With the aim of filling this gap in the literature, the present study investigated the relationship between metavariables (metaconceptual awareness, metaconceptual regulation, affective awareness, and affective regulation) and science achievement with the mediating effect of science self-efficacy through structural equation modeling. A total of 576 eighth grade students participated in the study. Results indicated that science self-efficacy partially mediated the relationship that metaconceptual regulation and affective regulation have with science achievement. In other words, students who monitor and evaluate their existing conceptions and follow, control, and adapt their emotions are likely to have high science self-efficacy and then high science achievement. In addition, metaconceptual awareness, metaconceptual regulation, and affective regulation positively predicted science self-efficacy, which was itself a positive predictor of science achievement. The findings imply that metavariables are essential components of science achievement via self-efficacy.