Completely rebuilt in 2008, the academy's primary building in Golden Gate Park covers 400,000 square feet (37,000 m2).

Although one aspect of the IBSS is available for viewing by museum patrons at the science "project lab" exhibit, most of the research happens in laboratories and facilities, "behind the scenes", and not observable by the public.

[3] There also is a strong emphasis on environmental concerns, with all the various departments collaborating closely to focus on systematic biology and biodiversity.

[15] Academy researchers study life around the world: a 2011 expedition to the Philippines discovered an estimated 300 species new to science.

[citation needed] To accommodate its increasing popularity, the academy moved to a new and larger building on Market Street in 1891, funded by the legacy of James Lick, a 19th-century San Francisco real estate mogul, entrepreneur, and philanthropist.

[citation needed] However, only fifteen years later, the Market Street facility fell victim to the 1906 San Francisco earthquake and three days of fire, which also wiped out all but a wheelbarrow full of the academy's library and specimen collections.

[20][21] In 1916, the Academy moved to the North American Hall of Birds and Mammals in Golden Gate Park, the first building on the site that was to become its permanent home.

[citation needed] Before the old building being torn down in 2005, there was a Life through Time gallery, housing a large display on evolution and paleontology.

[citation needed] Construction began on the new $500 million building on September 12, 2005, while the exhibits were moved to 875 Howard Street for a temporary museum.

[24] In May 2020, during the COVID-19 pandemic, the Academy announced that it would lay off 105 of its then 504 employees, furlough 96 others, and enact pay cuts among part of the rest.

[2] Due to the COVID-19 lockdown's effect on ticket sales, the organization was expecting its revenue to decrease by around $12 million (36%) in the next fiscal year.

[26] One critic praised the building as a "blazingly uncynical embrace of the Enlightenment values of truth and reason", and a "comforting reminder of the civilizing function of great art in a barbaric age".

The museum's central piazza lies beneath a massive glass ceiling on the roof, which opens to allow cool night air to flow into the building below; by using this kind of natural ventilation instead of air conditioning to regulate interior temperature, the building becomes more energy efficient.

Renzo Piano and SWA Group won the American Society of Landscape Architects (ASLA) Award in design in 2009.