His father, Joe T. San Agustin (1930-2011), was a longtime Guamanian politician who served as Speaker of the Guam Legislature. Joe S. San Agustin attended John F. Kennedy High School.[2] He later received a bachelor's degree in criminal justice from the University of Guam.[1]
On abortion rights, San Agustin stated that "I am anti-abortion, but I cannot support any measure that does not allow exceptions for victims of rape or incest, or if deemed medically necessary to save a life.".[1] In 2018, San Agustin co-sponsored legislation to introduce a 20-week abortion ban.[7]