Individual differences in self-regulation have been a topic of increased empirical research. However, few investigations have been conducted on how sub-components of self-regulation differentially predict education outcomes over time. We examined cognitive and behavior regulation as predictors of middle-school students' (n = 127) long-term academic achievement. It has been previously reported that behavior regulation, not cognitive regulation, predicts state standardized test scores in the first year (Modrek et al. 2019). However, here we show that after two years, this pattern flips in that cognitive regulation, not behavior regulation, predicts state standardized test scores for both math and English. We analyzed the mediating role of learning using structural equation modeling, suggesting the differing roles of self-regulation in education where certain facets may or may not affect students' long-term outcomes.