What aspects of writing are doctoral students metacognitive about when they write research articles for publication? Contributing to the recent conversation about metacognition in genre pedagogy, this study adopts a qualitative approach to illustrate what students have in common, across disciplines and levels of expertise, and the dynamic interplay of genre knowledge and metacognition in learning to write for research. 24 doctoral students in STEM (science, technology, engineering, and mathematics) were recruited from subsequent runs of a genre-based writing course and were interviewed within a 2-year period when they submitted an article for publication, 3 to 11 months after course completion. Over time and across disciplines, doctoral students' metacognition converges on four main themes: genre analysis as a "tool" to read and write, audience and the readers' mind, rhetorical strategies, and the writing process. Furthermore, these themes are extensively combined in the students' thinking, confirming conceptualizations of expertise as an integration of knowledge types. Metacognition of these themes invoked increased perceived confidence and control over writing, suggesting key areas where metacognitive intervention may be promising.