Metaphors are core cognitive resources which enable the learner to comprehend abstract concepts in terms of concrete and embodied ones. This study is a qualitative interpretivist study based on the conceptual metaphor theory (CMT) that aims to examine the use of CMT in the learning of abstract STEM concepts, and its impact on the learning and teaching process. The study uses qualitative data that encompasses classroom discourse, learner reflection and physics, mathematics and biology teaching content, and thematic analysis is used to derive four types of metaphors: flow metaphors, mechanistic metaphors, structural metaphors, and journey metaphors. Results reveal metaphors act as cognitive bridges, facilitating the relationship between previous knowledge and the learning of new concepts, and help learners to reason, visualize, and reflect metacognitively. The study emphasizes the significance of employing metaphors in education of STEM in an educative, purposeful and context-sensitive manner for conceptual learning.