In the 1989 the Loma Prieta earthquake hit and greatly damaged the academy buildings. As repairs were planned, they realized that it would take a long time to bring the buildings up to modern standards so that led to a complete overhaul.

Construction began on the new $500 million building on Steptember 12, 2005, while the exhibits were moved to Howard Street temporarily. The academy reopened with a free day on Steptember 27, 2008, which brought over 15,000 visitors. The new building was designed by architect Renzo Piano, which earned him the Urban Land Institute Award for Excellence. The new building is at the forefront of enviromentally friendly design and has many features like producing 50% less waste water, recycling rainwater for irrigation, using 60,000 photovoltaic cells, and supporting a green roof with an area of 2.5 acres. With the new building some things got removed like the insect room, fish roundabout, crystal and mineral hall, and the reptile and amphibian displays in the central court.