In 1997, the concession to design and build the highway was granted to the Brisa corporation. That same year, in relation to the proposed routes for the construction of the highway, the Instituto de Conservação da Natureza (ICN, Institute for Nature Conservation) stated that the Environmental Impact Assessment (EIA) for the Castro Verde Special Protection Area (SPA) was not "technically adequate, nor even viable, to ensure that birdlife would be conserved, as it only included minimization measures". Afterwards, the ICN ordered the company to reroute the Aljustrel/Castro Verde section of the highway, as the plan was to build it within 10 km of the Castro Verde SPA. It also recommended that the SPA be enlarged to the south of Castro Verde, which was to be preceded by a study on the bird species in the area. On January 19, 2000, with construction behind schedule and under growing pressure from the mayors of the Associação de Municípios do Algarve (AMAL, or the Association of Municipalities of the Algarve region), the Secretary for the Environment issued an order to go ahead with the Aljustrel/Castro Verde section on the condition that there be strict compliance with the minimization and compensation measures defined by the EIA. One month later, a public consultation on the EIAs for the two last sections of the A2 was held. For the environmental groups involved, the compensation measures proposed for these sections did not provide adequate safeguards.

This led the Grupo de Estudos de Ordenamento do Território e Ambiente (GEOTA), the environmental organization Quercus and the Liga para a Protecção da Natureza (LPN) to request that the European Union (EU) suspend the decision to allow the construction to proceed due to the significant population of several protected wild birds species in the Castro Verde SPA. Despite the EIA's negative findings and the existence of alternatives to the selected route for this section of the A2, Portugal chose the route that would affect an important Natura 2000 site the most. The A2 eventually was opened to traffic in July 2001, even though infringement proceedings initiated by the EU Commission after the complaint presented by the environmental organizations were still underway. In 2004, the EU Commission decided to lodge a complaint against the Portuguese state at the European Court of Justice (ECJ).

In October 2006, the European Court of Justice condemned Portugal for breach of the Birds and Habitats directives. The court found evidence that not only did the section of the A2 in question cause significant environmental impacts, but also that other alternative routes were ignored and not included in the study. It was also determined that the construction of the road should be compensated by the expansion of the Castro Verde SPA. In early 2008, the EC announced a "final warning" to Portugal to take measures to mitigate the negative impacts on two SPAs in the Alentejo region: Mourão-Moura-Barrancos and Castro Verde. In February 2008, legislation to expand these areas was approved by the Council of Ministers. 6.420 hectares were incorporated into the Castro Verde SPA, of which 2.034 ha are in Almeirim and 4.386 ha in Lombador-Figueirinha.