Researchers have expressed concern about the state of STEM education. To improve this situation, new pedagogies, such as blended learning, have been proposed and tested. The last decade has seen an increase in the use of blended learning to support learning; however, the effect of blended learning on learning remains unclear and often mixed. The two studies in this paper draw on data from pre-university science students in the following courses: (1) Electricity and Magnetism (E&M) and (2) Waves, Optics & Modern Physics (Waves). In study 1, the treatment group (blended learning coupled with two-stage quizzes & peer formative feedback) performed significantly higher than the control group (lecture format with online homework & instant feedback) in the standardized final exam. In contrast, in study 2, there was a non-significant main effect of groups, indicating that the treatment group (blended learning with online homework & instant feedback) and the control group (lecture format with online homework & instant feedback) performed similarly in the standardized final exam. The finding of study 1 suggests that the effect of an instructional pedagogical framework embedded in a blended learning context improves performance in STEM education. Whereas the finding of study 2 suggests that a blended learning context without incorporating any instructional framework or support for cognition other than the lecture is comparable to a traditional face-to-face course.