The application of smart technologies and applications is becoming increasingly common in the logistics processes of companies and supply chains. However, standard logistics indicators are still used to evaluate their performance, which contradicts the sustainable development strategy of many industrial enterprises and their supply chains. Thus, the article aims to design a methodology for selecting sustainability key performance indicators (SKPIs) suitable for assessing smart logistics and its technologies and applications. The research relies on cluster analysis of the SKPIs recommended in the relevant literature, frequency analysis of indicators used in practice and their comparison. The cluster analysis showed that the primary attention in the references is given to sustainability’s economic and environmental dimensions. Most frequently, the authors highlighted the importance of the following indicators: production-related costs and investments, planning performance and quality, customer satisfaction, energy efficiency, waste intensity and treatment, emissions, and resource efficiency. On the contrary, the frequency analysis corroborated that leading industrial enterprises paid more-or-less balanced attention to all areas of sustainability, but at the company level. The article’s primary result constitutes a methodology comprising six steps, respecting the results of the analyses carried out: (1) Sustainability objectives definition; (2) Establishing SKPIs cluster pool; (3) Definition of criteria for selecting SKPIs clusters; (4) Selection of SKPIs clusters; (5) Definition of SKPIs and their parameters; and (6) Development of SKPIs hierarchical structure.