Daylight plays a central role in synchronizing the human circadian system, exerting profound non-visual effects on physiology, cognition, and emotional well-being. While most research on these effects has relied on artificial lighting in tightly controlled laboratory settings, such conditions fail to capture the spectral and temporal complexity of natural light exposure in real-life environments. This paper introduces a novel experimental methodology designed to systematically compare the non-visual impacts of daylight and electric lighting properties under ecologically valid yet controlled conditions. The protocol employs a multi-day, semi-controlled design conducted in office-like settings, using carefully matched pairs of lighting conditions—two daylight-based and two electric light-based—to isolate optical and perceptual differences. By matching photopic illuminance and melanopic equivalent daylight illuminance (melEDI), the approach ensures non-visual response equivalence while allowing for controlled manipulation of temporal and spectral composition, light directionality, and visual context. Data are collected using a comprehensive array of sensors and questionnaires to assess physiological, neurological, cognitive, and behavioral outcomes. The protocol addresses methodological challenges such as dose-response matching, spectral calibration, and logistical coordination across multiple sessions and environments. Although no empirical results are reported, this methodological platform provides a crucial step toward disentangling the nuanced effects of real-world lighting dynamics on human functioning. By bridging the gap between laboratory control and environmental realism, it offers a foundation for future research and evidence-based lighting strategies to promote health, alertness, and well-being in built environments.