The relation between learners' metacognitive skills and conceptual understanding is often portrayed as an input-output relation when dealing with science, technology, engineering, and mathematics (STEM) and non-STEM disciplines. However, studies indicate that not all pedagogies yield positive correlations between learners' metacognitive skills and conceptual understanding, particularly in the science (S) strand of STEM. On the other hand, it has been revealed that self-organised learning environments (SOLEs) pedagogy incorporates the characteristics of some of the learning models that were found to induce positive correlations between learners' metacognitive skills and conceptual understanding in other non-STEM disciplines. Due to the lack of established research, particularly around the "S" in STEM, in the study reported on here we investigated the correlation between metacognitive skills and conceptual understanding under SOLEs pedagogy. We employed a quasi-experimental design which included 2 experimental and 2 control groups. Data were collected from 155 participants using the sciences (strand of STEM) performance test and metacognition self-assessment scale (MSAS) questionnaire. Data were statistically analysed using Pearson's product-moment correlation coefficient (r), means (?? ), and t-test. The results indicate a positive correlation between learners' metacognitive skills and conceptual understanding of sciences when SOLEs pedagogy was employed.