This article analyses the role of the European Union’s LIFE Clean Energy Transition (CET) programme in shaping patterns of small and medium-size enterprise (SME) participation in the green transition. The study applies a comparative approach, examining CET projects implemented in Lithuania and Germany during the period 2021 to 2024. The analysis focuses on project distribution, funding volumes, institutional composition, thematic scope, and SME involvement. The findings reveal significant differences between the two countries. Germany demonstrates a larger and more diverse project portfolio, with SMEs actively participating in technologically oriented and governance-related initiatives. In contrast, Lithuania’s participation remains more limited, and is concentrated primarily in capacity-building activities, with SMEs playing a more indirect role. The results indicate that the effectiveness of EU green policy instruments depends on national institutional capacity, innovation infrastructure, and administrative experience. The study contributes to the literature by providing a comparative empirical analysis of the LIFE CET programme, and highlighting uneven outcomes of EU green policy implementation across Member States.