Methods of multi-criteria decision making (MCDM) from operations research have been applied to provide information for making long-term decisions in the energy sector, and energy policy. For example, in sustainability evaluations, multiple conflicting criteria can be considered. While most MCDM approaches have been applied to evaluate energy systems in a single period, the multi-criteria evaluation of energy system evolution over time has received less attention. To evaluate such transition paths, multi-period MCDM approaches can be used. Because of long-term planning horizons, deep uncertainties need to be considered. Based on prior multi-period MCDM approaches, this paper provides an extension of the outranking approach preference ranking and organization method for enrichment evaluations (PROMETHEE) for multi-period evaluations in deep uncertainty settings. In order to adequately address the consideration of uncertainties and to obtain an additional level of information, a multi-period PROMETHEE approach and scenario planning are combined. In an illustrative example, this method is applied to a case study from the German energy sector regarding a renewable energy transition. This highlights the potential interactions of a multi-period perspective and the consideration of external scenarios in the decision-making process.