Higher education institutions increasingly seek learning environments that support diverse cognitive needs while advancing sustainability through the adaptive reuse of existing buildings. Although research demonstrates that environmental factors such as lighting, acoustics, spatial organization, flexibility, and environmental quality influence learning and well-being, architects still lack practical methodologies for translating interdisciplinary evidence into design decisions. This study proposes an evidence-informed neuro-inclusive design methodology for adaptive reuse university learning environments. Building on a previously developed framework comprising five design principles—Sensory Regulation, Lighting Control, Spatial Predictability, Flexibility, and Emotional Comfort—the methodology was comparatively applied to three adaptive reuse learning environments at the University of Naples Federico II. A qualitative multiple-case study approach examined how the framework informed architectural decision-making across different spatial configurations, educational functions, and heritage constraints. The findings demonstrate that the framework provides a consistent evidence-informed design process while generating context-specific architectural solutions rather than standardized outcomes. The study contributes a transferable methodology that bridges interdisciplinary knowledge and architectural practice, supports the design of cognitively accessible learning environments, and demonstrates how neuro-inclusive principles can be integrated into adaptive reuse projects without compromising the architectural integrity of historic educational buildings.