The purpose of this study is to investigate into the possibility of utilizing socio-scientific issues as a vehicle to promote students’ metacognitive regulation, self-efficacy and conceptual understanding in an ecology classroom in Hong Kong. There has been little research to assess how these constructs are influenced by an issue-based inquiry classroom environment set in ecological context, and how these constructs interact with each other. The researcher has designed a metacognitive-rich environment for learning through a socio-scientific issue in a high school ecology classroom. Students’ perceptions about the metacognitive orientation of the classroom environment were assessed by the Metacognitive Orientation Learning Environment Scale (Science) to provide evidence for the validity of the lesson design in creating a metacognitive-rich environment. The effect of embedding explicit metacognitive tasks into a socio-scientific issue on students’ self-efficacy and metacognition were assessed through a quasi-experimental study using the Motivation Strategy for Learning Questionnaire and post-lesson individual interviews. 54 students from a Hong Kong long-established boy school participated in this study. The changes of the dependent variables under study were analyzed using an independent samples t-test and a 2x2 mixed-design analysis of variance to indicate the effect of this specially designed intervention in the biology classroom. The quantitative results suggested the intervention has created significant positive effects on students’ metacognitive regulation and self-efficacy but not conceptual understanding. Results from the multivariate analysis of variance and Pearson correlations suggest that the three dependent variables under study are correlated. To assist in the interpretation of the quantitative findings, individual interviews with students in the intervention group were analyzed thoroughly based on the concurrent triangulation approach. The interview results