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Pedagogical knowledge has been taught mainly through direct instruction in many science teacher preparation (TP) programs, which could lead to the problems such as Pre-service Teachers’ (PST) impersonality and low motivation. There also exists a gap between the tremendous amount of information PSTs are exposed to and the limited time they have in TP programs. This study presents the design of Scaffolding Pedagogical Instruction (SPI) and examines its impact on PSTs’ competence and disposition for science teaching. This quasi-experimental study comparing SPI and direct instruction suggests that SPI, as an inquiry-oriented approach, is equally effective in promoting PSTs’ competence of teaching as direct instruction. This study also discusses the challenges faced by teacher educators while implementing SPI.