While research on metacognition, self-regulation and self-regulated learning is quite mature, these studies have been carried out with varying methodologies and with mixed results. This paper explores the ontological and epistemological assumptions of theories, models and methods used to investigate these three constructs to examine the underlying assumptions of all three. Using oft-cited theories and models of the three constructs along with highly cited studies identified in a previous review of these constructs, this paper examined facets of two popular frameworks: Cartesian-split-mechanistic tradition (CSMT) and the relational tradition specifically looking at the role of intra-individual development, the inclusiveness of categories and notions of causality in these theories, models and methods. While the theories and methods contained elements of both traditions, methods to investigate these constructs relied almost exclusively on assumptions from CSMT. Future directions for research include incorporating more studies examining intra-individual change and multiple notions of causality. Future directions for practice include better contextualisation of research results to strengthen the link between theory and practice.