The Natura 2000 network, the pillar of biodiversity conservation in Europe, still shows some knowledge gaps after almost 30 years since its implementation. As birds are a taxonomic group that is underrepresented in the literature related to Natura 2000 compared to their importance in the EU Directives, this review investigated the characteristics of the scientific research dedicated to birds in relation to Natura 2000. This review focused on 169 peer-reviewed articles covering a period of 25 years (1995–2019). Most studies were set within single Natura 2000 site or regions within countries, and concerned terrestrial habitats, particularly wetlands. The terrestrial Mediterranean biogeographical region and marine Atlantic region had the greatest number of publications, while Spain, Italy, and France were the countries with the highest number of reviewed articles. The number of publications was correlated to Natura 2000 coverage at both country and biogeographical region level. Bird species were studied mainly at a community or single-species level and most publications studied distribution and occurrence of the bird species of interest, while very few assessed the conservation status of the species. Only a few articles set within Natura 2000 sites addressed the issues of habitat suitability for birds or the effectiveness of conservation efforts. Both Annex I and non-Annex I bird species were examined in the literature, with most species having decreasing population trends at the European scale. Future research on bird conservation and Natura 2000 should focus on marine ecosystems as well as habitats that have received less attention despite their important role in a changing future (alpine and urban types). Moreover, future studies should encompass larger spatial scales and those species for which status and trends are still not thoroughly investigated. Finally, it would be important to enhance research efforts on the conservation status and effectiveness in relation to the network.