This paper reports about the effect of an innovative, context-based science teaching and learning program on student intrinsic motivation. The intervention aimed at promoting Inquiry-Based Science Education (IBSE) in close collaboration with teachers throughout the academic year by developing and implementing socio-scientific, context-based, innovative, three-stage modules. The Motivational Learning Environment (MoLE) model and questionnaire was used to measure the impact of context-based science modules on the motivation of sixth to eleventh graders at secondary schools in Georgia. Students’ wish- to reality-differences data were analyzed concerning the seven dimensions of the Motivational Learning Environment model. As a result of a one-year training program we observed statistically significant differences in two dimensions for the treatment classes (compared to the control classes) in pre- and post-test results. The study suggests more education systems should consider context-based, socio-scientific science teaching as a leading approach to enhance students’ motivation and interest in science education.