Ports are important and central hubs for logistical activities in transportation chains that contribute to economic growth. Nevertheless, port activities are associated with undesirable impacts such as energy consumption and air pollutant emissions. Various policy instruments and measures have been developed and adopted to reduce energy consumption and emissions from ports. In an effort to manage all undesirable impacts of port operations, the search for best practices has proven to be an effective approach. This study examines one- and two-stage Data Envelopment Analysis (DEA) models for measuring port environmental efficiency. The adequacy of the models was analyzed using two case studies, i.e., the port of Koper and port of Dublin. The results of the study provided the best practices and the main differences between one-stage and two-stage models. Distance metrics were used to identify the necessary improvements of inefficient decision-making units (DMUs) to achieve the best practices.