The current study examined self-organized learning environments (SOLEs) pedagogy as a conduit to learners' metacognitive skills and conceptual understanding in physical sciences and science, technology, engineering, and mathematics (STEM) as a whole in Capricorn District of Limpopo Province of South Africa. The aim was based on ongoing debates related to integrating technology and metacognitive skills in STEM education to improve educational outcomes. Anchored upon the aim and through experimental (one urban and one rural) groups and control (one urban and one rural) groups, the study employed a non-equivalent quasi-experimental (control group) design to glean and analyze data from 155 selected participants through a stratified sampling method. Data were collected using physical sciences pre- and post-tests and metacognition self-assessment scale questionnaire. Data analysis employed descriptive (mean [M], standard deviation, and effect size) and inferential (parametric t-test) analysis. The findings indicate that the mean gain score (M=6.37) of the experimental groups (that were taught through SOLEs pedagogy) was higher than that of their counterparts (M=2.60) in the control groups with a p-value (p=0.037) that is less than 0.005. Similarly, in terms of conceptual understanding, the findings indicate that the experimental groups improved significantly more than the control groups at a significant p-value of 0.00. Finally, the study concludes that SOLEs pedagogy improves learners' metacognitive skills that, in turn, enhance conceptual understanding of physical sciences content. Furthermore, the current study recommends further longitudinal studies with larger sample sizes to explore SOLEs pedagogy in STEM.