Inquiry-based teaching is considered as contributing to content-related, procedural, and epistemic learning goals of science education. In this study, a quasi-experimental research design was utilized to investigate to what extent embedding inquiry activities in an explicit and an implicit instructional approach fosters students' ability to engage in three practices of scientific investigation (POSI): (1) formulating questions and hypotheses, (2) planning investigations, (3) analyzing and interpreting data. Both approaches were implemented in a classroom-based intervention conducted in a German upper secondary school (N = 222). Students' procedural knowledge of the three POSI was assessed with a paper-pencil test prior and post to the intervention, their content knowledge and dispositional factors (e.g., cognitive abilities) were gathered once. Results show that not only explicit but also implicit instruction fosters students' knowledge of POSI. While overall explicit instruction was found to be more effective, the findings indicate that the effectiveness depends considerably on the practice addressed. Moreover, findings suggest that both approaches were equally beneficial for all students regardless of their prior content knowledge and their prior procedural knowledge of POSI. Potential conditions for the success of explicit and implicit approaches as well as implications for instruction on POSI in science classrooms and for future research are discussed.