In pillar 1 of the EU-BDS 2030, the EU commits to protecting nature by improving and widening its network of protected areas (PAs). By 2030 it aims to legally protect a minimum of 30% of EU land area and of EU sea area, and to strictly protect at least a third of these PAs, including all primary and old-growth forests. It aims to effectively manage and monitor all PAs, defining clear conservation objectives and measures, and to integrate ecological corridors as part of a Trans-European Nature Network. Many of these goals are supported and implemented by the New EU Forest Strategy for 2030, the initiative (2021) for an action plan to conserve fisheries resources and protect marine ecosystems (pending), the new climate strategies and laws, and actions and strategies in other sectors under the European Green Deal.

The EU Nature Directives, namely the Habitats Directive (1992) and Birds Directive (2009), require MS to ensure both the physical protection of individual specimens as well as the conservation of core breeding and resting sites for rare and threatened species under the Natura 2000 network, the world's largest coordinated network of protected areas covering over 26 000 sites. Over 1000 animal and plant species, as well as 200 habitat types, are protected under the Habitats Directive via inclusion in Natura 2000, strict protection regimes, and other measures. The Birds Directive protects around 500 wild bird species naturally occurring in the EU via measures ranging from Special Protection Areas, restrictions on hunting, trade and other activities that threaten birds, to promoting research on protection and management. A fitness check (2016) of the Birds and Habitat Directives concluded that, while both remain highly relevant within the broader framework of EU biodiversity policy, full achievement of their objectives would depend on substantial improvement in implementation. The EU Action Plan for nature, people and the economy was developed and adopted (2017) to improve implementation. However, the evaluation (2022) of the EU Biodiversity Strategy to 2020 concluded that only 15% of habitat assessments under the Habitats Directive show good status (a further deterioration since 2010). While it is estimated that about 93% of the mapped primary and old-growth forests are part of the Natura 2000 Network, with 87% strictly protected, these figures should be considered with caution due to mapping deficits and an unclear legal framework. Strict protection of primary and old-growth forests is an urgent priority requiring robust and up-to-date spatially-explicit data, and an efficient monitoring system

The Natura 2000 network forms the backbone of EU green infrastructure (GI), and lies at the core of the EU GI Strategy (2013). GI is a strategically planned network of natural and semi-natural areas with other environmental features designed and managed to deliver a wide range of ecosystem services. GI also includes green spaces outside Natura 2000, such as parks, gardens, hedges, green verges and high-diversity agricultural landscapes, green roofs and walls, eco-bridges and fish ladders. In 2019 some progress was reported in GI deployment, but it needs to be scaled up. In particular it was noted that the Nature Directives are less effective in maintaining GI outside of Natura 2000.

The EU pollinators initiative (adopted in 2018) was the first-ever EU framework directed at tackling the decline of wild pollinators. It proposed ten specific actions categorised under three priorities, to be implemented until 2020 with a long-term perspective towards 2030. In 2021 significant progress was reported in its implementation, and in policy enablers to monitor pollinator species and the drivers of their decline. However the progress report pointed to significant remaining challenges in tackling these drivers, in particular in addressing the loss of habitats in farming landscapes, and the impacts of pesticides. The report also called for a pollinator-information system and tailored research to support the Initiative. The ensuing 12-week public consultation in 2022, led to the revised initiative A new deal for pollinators in January 2023, with eleven specific actions to be achieved by 2030, categorised under slightly revised priorities: (1) Improving knowledge of pollinator decline, its causes and consequences; (2) Improving pollinator conservation and tackling the causes of their decline; and (3) Mobilising society and promoting strategic planning and cooperation at all levels. The EU-BDS 2030, Farm to Fork Strategy and Zero Pollution Action Plan are expected to substantially reinforce actions to protect pollinators. The Nature Restoration Law (2022) aims to reverse pollinator decline by 2030.

The EU regulates the role of zoos in biodiversity conservation via the Zoos Directive (1999). A recent evaluation (2018) declared it plays a small but necessary role within a wider legislative framework, and is coherent with EU legislation on biodiversity conservation. However, improved implementation is required to achieve its full potential.

Regarding marine ecosystems, the Marine Strategy Framework Directive (MSFD, 2008) aims at more effective protection of the marine environment, supplemented by revised criteria and methodological standards (2017) for implementation by MS. The report on the implementation of the MSFD (2020) shows that, while the EU’s framework for marine environmental protection is one of the most comprehensive and ambitious worldwide, it needs to be beefed up to be able to tackle predominant pressures. It has been followed up with an initiative (2021) for an action plan to conserve fisheries resources and protect marine ecosystems (pending) and other actions under the common fisheries policy. In 2022 the Commission adopted an implementing regulation closing 87 areas to all bottom fishing gears in the EU waters of the North-East Atlantic, thus protecting 57 vulnerable deep-sea ecosystems, in line with the  Deep-sea access regulation of 2016.