Policy initiatives from the United Nations and EU institutions have emphasized the need for higher education institutions (HEIs) to fulfil a significant role in green transitioning. However, they tend to fall short of the achievement of this objective. Multiple studies indicate that HEIs assign high importance to the integration of environmental sustainability on a strategic level but generally lack dedicated policies of integration in operational aspects. This paper’s research aim is to provide a meta-study that reviews, analyzes, and assesses the state of the art on research on HEI sustainability. The paper also contributes to the state-of-the-art by mapping institutional sustainability self-assessment models, tools, and guidelines in four prominent research areas: (1) sustainability integration in educational activities, pedagogical perspectives, and systemic transformations; (2) benchmarking sustainability of organizational transformation and operational optimization, and links between developmental priorities and educational settings; (3) whole-system approaches focusing on the design and implementation of whole-institution sustainability plans; and (4) HEI sustainability culture and operations. The paper’s final contribution is the presentation of best practices and emerging trends in the literature. These practices were selected on the following qualitative methodological criteria based on the systems-thinking approach to whole-institution assessment: (1) the effectiveness of self-assessment models, tools, and guidelines in each respective research area; (2) the degree of integration of systems thinking and/or modeling; and (3) the incorporation of qualitative indicators for stakeholder engagement.