The metacognitive strategies of planning, monitoring, and evaluating can be promoted through systematic reflection to drive self-directed, lifelong learning. This article reports on a three-year study on systematic written reflection within an undergraduate Fluid Mechanics course to promote planning, monitoring, and evaluation. Students were prompted weekly to reflect on their in-class problem-solving, classroom and exam preparation, performance, behaviors, and learning in a flipped classroom at a large southeastern U.S. university. In addition, they received intentional instruction on how to plan, monitor, and evaluate their problem-solving during class. To enable a comparative assessment, a flipped classroom without these interventions was also implemented as a non-experimental cohort. The cohorts were compared using a final exam, concept inventory, and the Metacognitive Activities Inventory (MCAI). The MCAI indicated a significantly higher positive change (pre- to post-course) in self-regulatory behavior for the experimental cohort ( p = 0.037). The weekly reflections were studied using an inductive content analysis to assess students’ self-regulatory behaviors. They were also used to investigate statistical associations between reflection content and course outcomes. This revealed that academic self-discipline via planning, monitoring one's work, or being careful and diligent may be as aligned with course performance in STEM as is practice with the problem-solving itself. The effects for the final exam in the experimental cohort were positive overall as well as statistically or practically significant for various demographic strata. These results provided evidence for the potential enhancement of course performance with metacognition support. A positive shift in students’ perspectives regarding the value of the reflection questions was observed throughout the study. Therefore, as an implementation guide for other educators, the reflection questions and any changes made in posing them to students are discussed chronologically. Overall, the study points to the desirability of providing metacognition support in a STEM course.