To achieve the ambitious CO2 emission reduction targets set by the Sustainable Development Goals, it is crucial to act on cities. Indeed, cities are responsible for 67% of the world’s primary energy consumption and about 70% of energy-related CO2 emissions. To support the urban energy transition, a broad implementation of zero-emission districts or, even better, positive energy districts (PEDs) is expected. PEDs can be defined as energy-efficient and energy-flexible urban areas that aim to provide a surplus of clean energy to the city by using renewable energies. However, in developing the PEDs concept, it is necessary to consider not only the technical issue of energy systems but also the environmental, social, and economic spheres. To be effective, it is important to provide decision-makers with tools such as Urban Sustainability protocols for PEDs, which can effectively assess the complexity of the impacts a PED might have on other urban transformations from a multi-stakeholder perspective. LEED for Neighborhood Development, BREEAM Communities, and CASBEE for Cities are the most widely used and known protocols in the world for the evaluation of districts. These certification protocols were established before the concept of PEDs and, therefore, are not considered. However, they exhibit some shared characteristics which permit the evaluation of PEDs’ sustainability. In fact, through this research, an attempt is made to analyze how the implementation of sustainability protocols in existing PED projects can improve sustainability, but also how PED projects can improve evaluation systems through interventions that have not been considered so far. To test a methodology that could be extended in future case studies, an analysis of three of the world’s best-known certification systems, LEED-ND, BREEAM-CM, and CASBEE-UD, was conducted on two completed PEDs case studies, Tampere and Salzburg.