Pre-service teachers face challenges in learning how to implement inquiry-based learning to enhance students' higher order thinking skills (HOTS) effectively. This study describes pre-service science teachers' instructional practices to teach HOTS related to key aspects of inquiry. The study group comprised 15 undergraduate pre-service teachers who enrolled in the thinking course of a 5-year teacher enhancement program. The pre-service teachers' lesson plans and teachers' self-reflections on their practices were collected, and then analyzed by descriptive statistics and inductive analysis. Findings indicated that the pre-service teachers were most likely first, to advance their level of inquiry; and second, to shift their teaching practices from focusing on science as a process to be learned about that primarily represents the inquiry features of only evidence and explanation to the inclusion of all five features of inquiry. Moreover, pre-service teachers were able to design creative and reasoning-enriched activities. They promoted the following aspects of inquiry: Asking divergent questions on a problematic situation, having students think originally for investigation, building and refining a model or design, and generate and test hypotheses reasonably leading to causal inferences. The findings from this methods course point toward future directions for effective courses that develop pre-service teachers' practices aimed to promote students' thinking skills.