Designing modern systems requires technical knowledge and sustainability competencies from engineers, as almost every system or product designed has a sustainability impact. This gained additional significance after adopting the Sustainability Development Goals in 2015 and their subsequent integration into the activities of enterprises and other entities and the products and services they offer. For this reason, the study’s main goal was to determine the role of sustainability competences in activities performed by systems engineers. Sustainability competences and systems engineering competencies were analyzed. A significant overlap in many areas was found. Subsequently, the perception of these competencies by representatives of enterprises was examined. The results indicate that system engineers’ perception of sustainability competences is not uniform, particularly depending on the size of the enterprise and position in the company hierarchy. Engineering team leaders and management pay more attention to soft skills. The study’s results may help understand the relationships between competencies, support the development of HR processes, and entities offering training programs for employees at different career stages.