Metacognitive skills can have enormous benefits for students within engineering courses. Unfortunately, these metacognitive skills tend to fall outside the content area of most courses, and consequently, they can often be neglected in instruction. In this context, previous research on concept mapping as a teaching strategy points to meaningful learning. The purpose of this innovation paper is to report an application of concept mapping (1) to facilitate metacognition steps in students, and (2) to identify the muddiest points students struggle with, during both in-person and online instruction of a problem-solving-based biomedical engineering course. This innovation article also looks at the usefulness of concept mapping through instructor and student perceptions and students' class performance. The entire concept mapping intervention was conducted during weeks 8-10 of the Spring 2019 in-person quarter and during weeks 3-4 and 8-10 of the Spring 2021 online quarter. The exercise involved concept mapping, explanation and discussion with peers, and answering structured reflection prompts. Each concept map activity was contextualized to the metacognitive knowledge domain of the revised Bloom's taxonomy. The average class performance was compared between students who completed concept mapping vs. those who did not, using a t-test and one-way ANOVA at alpha = 0.05 significance level followed by a Tukey HSD test. Students' concept maps and reported answers were analyzed qualitatively following the concept mapping intervention. During the Spring 2019 in-person quarter, 59.30% of students completed concept mapping with reflection, whereas 47.67% completed it in spring 2021 online instruction. A two-tailed, unpairedThe online version contains supplementary material available at 10.1007/s43683-022-00066-3.