This study aimed at improving the decision-making (DM) skills of 11th graders by incorporating a DM framework, visualisation tools, collaboration, and metacognitive guidance into a socioscientific issue context. Two classes, the experimental group (embedded metacognitive guidance, N = 42) and the comparison group (no metacognitive guidance, N = 32), were involved in the implementation of the experimental methodology. An open-ended test and worksheets were developed to assess the students' DM skills. The results indicated that the two versions of the DM learning modules had similar effects on the improvement in the students' DM skills, but there were significant differences in their overall skills in DM (Z = -6.410, p < 0.001), generating criteria (Z = -6.956, p < 0.001), and evaluating DM results (Z = -2.533, p < 0.011) based on the student responses on the worksheets. These findings indicate that further studies need to explore the mechanism of metacognitive guidance for students with different socioscientific issue DM skills in e-learning environments.