As an initial effort to reorient the current Malaysian chemistry curriculum, green chemistry was developed. In this study for the purpose of investigating the effectiveness of the green chemistry curriculum on secondary school students’ understanding of chemistry concepts a quasi-experimental design was used. One-group pretest posttest design was used to measure the changes in the motivation before and after the treatment. Two classes were randomly assigned to experimental (N = 35) and control group (N = 32). Following the intervention, an ANCOVA with pre-test as the covariate showed the experimental group achieved significantly higher (M E = 23.40, SD E = 1.39) than the control group (M C = 12.78, SD C = 1.71), F = 1,018.26, p < 0.0001. The effect size was very large, d = 18.7. The unbiased JCS Bayes factor (JCS ≪ 1/100) suggests that the evidence is substantial in favor of the alternative hypothesis of group differences. The analysis of the pre-post semi-structured interviews, concerning motivation found that a significant number of students changed from low to high self-efficacy belief, high task value belief, transformed their goals of learning toward mastery orientation, and were more interested toward learning chemistry after the intervention.