As offshore wind energy expands in Europe, maritime planners increasingly need to consider the potential effects of these activities on the different types of marine protected areas (MPAs), including Natura 2000 sites. The aim of this article is to critically review the initial development of offshore wind energy inside and/or in the vicinity of Mediterranean Natura 2000 sites and other types of MPAs. The western Mediterranean Sea is taken as an example as this is where most of the offshore wind developments have been proposed. In order to open up discussion of offshore wind energy policy and guide ecological research that supports holistic decisions regarding offshore wind farm (OWF) installation in the region, we (i) outline the context of Natura 2000 and other MPA policy in the Mediterranean for OWF development, (ii) summarize the potential impacts of OWF on EU-protected habitats and species, (iii) assess the interactions of OWFs, the Natura 2000 sites, and other MPAs, and (iv) propose recommendations to approach OWF development in the Mediterranean in order to safeguard the Natura 2000 sites and other MPAs. After documenting the potential overlaps between OWFs and MPAs in the western Mediterranean, we recommend OWFs be placed outside Natura 2000 and other MPA sites, including their buffer zones. We also advocate for rigorous and independent Appropriate Assessments to be carried out for OWF proposals that could affect protected areas.