Traditionally, research in educational psychology has neglected the physiological foundations of motivation, emotion, engagement, and learning. Recent studies have made substantial progress to more fully consider physiological processes, as documented in the contributions to this special issue. In this commentary, I summarize their findings, discuss strengths and weaknesses, and outline directions for future research. The studies showcase how physiological indicators can be integrated in research in educational psychology. The resulting findings document links between cardiovascular, electrodermal, and hormonal parameters as well as physical activity and a range of mental and behavioural processes in educational settings. Together, they attest to the critical role of physiological processes in students' and teachers' engagement. However, most of the studies used small samples and correlational designs, and not all of the findings were consistent. To inform theory and practice in evidence-based ways, we need to make further headway in building a cumulative, coherent knowledge base. To this end, it may be helpful to more precisely specify the status of physiological indicators; secure construct symmetry of physiological, mental, and behavioural variables; use causal designs and within-person analysis; include sufficiently powered samples of participants and measurement occasions; employ multiple indicators and assessments to increase reliability and specificity; define the time windows and lags of assessments that are suited to capture physiological processes and their functions; and consider the role of socio-cultural contexts.