Formal teacher preparation programs are facing the challenge of ineffective instruction of educational theories. It is partly because educational theories are taught through direct instruction, which could lead to problems such as impersonality and low motivation of pre-service teachers. In addition, it is also an unwieldy task for teacher educators to cover meaningfully a tremendous amount of theories through direct instruction within a limited time. This study presents an innovative approach of Inquiry-based Pedagogical Instruction (IPI) as a possible solution. The IPI approach has two key features: explicit modeling and scaffolding. In this quasi-experimental study, I compare IPI and direct instruction in promoting pre-service teachers' competence in terms of their knowledge associated with science teaching and their disposition in terms of their sense of belonging to science and science teaching. The participants are 39 pre-service teachers in Phase 1 with 23 of them receiving IPI and the other 16 receiving direct instruction and 92 pre-service teachers in Phase 2 with 42 receiving IPI and 50 receiving direct instruction. The results from two-way ANOVA and effect size analyses suggest that IPI is a promising alternative to direct instruction for the instruction of pedagogical knowledge. IPI has the potential to empower pre-service teachers with the competence and disposition with which they are capable and willing to construct their knowledge of teaching. Implications for future research are also discussed.