The development of student metacognition has the potential to provide some of the greatest learning gains in science education, even outstripping the contribution of general intelligence. While models for metacognition are in broad agreement about their nature, they vary widely in essential elements and the relationships between them, especially between metacognitive knowledge and metacognitive skills. Recent systematic literature reviews have not untangled the concept of metacognition as they are not suited to crafting a synthesised conceptualisation for a controversial topic. This article, then, presents an integrative literature review of metacognition studies that draws together metacognitive knowledge and metacognitive skills into a hierarchical framework. The framework comprises, from the foundational level, metacognitive knowledge, called self-Aware of cognition, then various metacognitive skills; self-Monitor cognition, self-Evaluate cognition, self-Regulate cognition and self-Transfer cognition (AMERT). As a preliminary test of its viability, the AMERT framework is used to analyse interview data in which there was evidence of rich metacognitive thinking by students in the fourth, research-focused, year of a science degree. Rich epitomising statements were found in interviews for each level of the AMERT hierarchy, providing tentative evidence of its viability for understanding metacognitive processes when students learn in science.