The construction cost of the building was $144 million.[11]​ The architect's decision to eliminate the usual HVAC system saved $11 million.[13]​ At the same time, the non-functional use of extensive metal sunshades folded at ground level, which some believe are purely for aesthetic reasons and required significant galvanized steel reinforcements, added several million dollars to the cost of the project.[11]​.

The Morphosis design was chosen, at least in part, for its projected energy efficiency, a requirement of the General Services Administration (GSA). However, at the time of its design the GSA did not require LEED certification, and the building was not evaluated for this certification until after its construction; the result was negative. Mayne said, “I wasn't arrogant, but I was confident: I just assumed we would get [LEED's highest] platinum certification. “All of a sudden we went through LEED and it didn’t work.” Ultimately, the building only achieved LEED silver certification, two levels below platinum.[14]​.

The building has been criticized by its employees for being dysfunctional. According to one employee interviewed by BeyondChron.com, "workers try to alleviate the heat by opening the windows, which not only causes papers to fly, but, depending on the distance from the window, makes it virtually impossible to create a stable temperature for all workers [...] some employees have to use umbrellas to protect their cubicles from the sun."[14]​

Mayne believed that the federal government should be a model in promoting worker health and physical exercise. This led him to specify that passenger elevators only stop on one in every three floors, which means that a good part of the workers and visitors have to go up or down one or two floors of the stairs to reach their destination. There are also elevators for people with reduced mobility that stop on all floors, but they have become commonly used also by people without mobility problems, causing congestion.[14]​.

Unlike most large government office buildings, the San Francisco Federal Building does not have a cafeteria within the building itself. Instead, the cafeteria was placed just outside the building, in the public plaza, again due to the architect's belief that this would encourage employees to walk, interact with each other, and improve their health, a situation that appears not to be appreciated by some of the two thousand four hundred employees working in the building.[14]

In 2010, the GSA commissioned a survey to determine the satisfaction of employees working in twenty-two federal buildings across the country, including the San Francisco Federal Building. The buildings included in this study achieved satisfaction scores between 13% and 98%; Seventeen of the twenty-two buildings achieved greater than 50% satisfaction. While incorporating many green concepts more aggressively than other buildings, the building with the lowest employee satisfaction was the San Francisco Federal Building, at just 13%; the next least satisfactory scored 26%. The building obtained scores significantly lower than the median in the categories of thermal comfort, lighting and acoustics.[9]​.

In 2020, then-President Donald Trump issued an executive order “on promoting beautiful federal architecture.” This order mentions the building as an example of unsatisfactory design, stating that "to design the San Francisco Federal Building the GSA chose an architect who describes his designs as "art for art's sake" architecture, designed primarily to be appreciated by other architects. While elite architects praised the result, many San Franciscans consider it one of the ugliest buildings in their city.”[15]​ This executive order was revoked by President Joe Biden in February 2021.[16]​.

The construction cost of the building was $144 million.[11]​ The architect's decision to eliminate the usual HVAC system saved $11 million.[13]​ At the same time, the non-functional use of extensive metal sunshades folded at ground level, which some believe are purely for aesthetic reasons and required significant galvanized steel reinforcements, added several million dollars to the cost of the project.[11]​.

The Morphosis design was chosen, at least in part, for its projected energy efficiency, a requirement of the General Services Administration (GSA). However, at the time of its design the GSA did not require LEED certification, and the building was not evaluated for this certification until after its construction; the result was negative. Mayne said, “I wasn't arrogant, but I was confident: I just assumed we would get [LEED's highest] platinum certification. “All of a sudden we went through LEED and it didn’t work.” Ultimately, the building only achieved LEED silver certification, two levels below platinum.[14]​.

The building has been criticized by its employees for being dysfunctional. According to one employee interviewed by BeyondChron.com, "workers try to alleviate the heat by opening the windows, which not only causes papers to fly, but, depending on the distance from the window, makes it virtually impossible to create a stable temperature for all workers [...] some employees have to use umbrellas to protect their cubicles from the sun."[14]​

Mayne believed that the federal government should be a model in promoting worker health and physical exercise. This led him to specify that passenger elevators only stop on one in every three floors, which means that a good part of the workers and visitors have to go up or down one or two floors of the stairs to reach their destination. There are also elevators for people with reduced mobility that stop on all floors, but they have become commonly used also by people without mobility problems, causing congestion.[14]​.

Unlike most large government office buildings, the San Francisco Federal Building does not have a cafeteria within the building itself. Instead, the cafeteria was placed just outside the building, in the public plaza, again due to the architect's belief that this would encourage employees to walk, interact with each other, and improve their health, a situation that appears not to be appreciated by some of the two thousand four hundred employees working in the building.[14]

In 2010, the GSA commissioned a survey to determine the satisfaction of employees working in twenty-two federal buildings across the country, including the San Francisco Federal Building. The buildings included in this study achieved satisfaction scores between 13% and 98%; Seventeen of the twenty-two buildings achieved greater than 50% satisfaction. While incorporating many green concepts more aggressively than other buildings, the building with the lowest employee satisfaction was the San Francisco Federal Building, at just 13%; the next least satisfactory scored 26%. The building obtained scores significantly lower than the median in the categories of thermal comfort, lighting and acoustics.[9]​.

In 2020, then-President Donald Trump issued an executive order “on promoting beautiful federal architecture.” This order mentions the building as an example of unsatisfactory design, stating that "to design the San Francisco Federal Building the GSA chose an architect who describes his designs as "art for art's sake" architecture, designed primarily to be appreciated by other architects. While elite architects praised the result, many San Franciscans consider it one of the ugliest buildings in their city.”[15]​ This executive order was revoked by President Joe Biden in February 2021.[16]​.