Two pivotal components of the EU’s climate policy are the protection of biodiversity and the promotion of renewable energy sources (RES). However, those two policies might clash, since the implementation of RES projects has the potential to negatively impact biodiversity. Following a doctrinal approach to legal research, this study aims to examine how could RES promotion and biodiversity protection be reconciled, by analyzing their legal interplay under Article 6(3) and (4) of the Habitats Directive (HD). According to the former every project that is likely to have significant effects on a Natura 2000 site, is subject to an assessment and may be authorized only if it is established that it will not affect the integrity of Natura 2000 sites. According to the latter, projects that are proved to adversely affect Natura 2000 sites may still be authorized provided that certain conditions are met. One of the issues identified is that the appropriate assessment procedure under Article 6(3) HD entails a very high standard of proof regarding the effects on protected sites, which may be unrealistic for certain RES projects, like novel and marine technologies. Moreover, the linkage between Articles 6(3) and (4) HD might result to the paradox of small-scale novel RES projects, with uncertain but probably limited impact on protected sites, not being authorized based on Article 6(3) HD and not being able to satisfy the conditions of Article 6(4) HD either, while large-scale novel RES projects, with uncertain but potentially extensive adverse effects on protected sites, would be authorized based on Article 6(4) HD. Those weaknesses could be averted by prioritizing the authorization of small- over large-scale RES projects characterized by uncertainty as to their effects on protected sites and imposing post-implementation continuous monitoring, data gathering and adaptation in the form of mitigating and compensatory measures.