[3] In response to this, Martin Luther King Jr. on behalf of the MIA, announced that the Association would attempt to end racial segregation in Montgomery public schools by having large numbers of black children apply for admission to white schools in order to provide test cases which might allow a judge to declare the Alabama Pupil Placement Act unconstitutional.

In 1970 the Academy adopted an explicit policy stating that race would not be considered in admissions[11] as required by Internal Revenue Service regulations.

[2] According to then-headmaster James Adams, although there had previously been no written statement to that effect, the Academy had never used race as a basis for admissions.

[12] In 1972, federal Judge Frank M. Johnson, whose son John was a student at the Montgomery Academy,[13] enjoined the city from continuing this practice,[14] writing that "In allowing private academies to use city facilities, Montgomery is providing aid to private, segregated schools, thus facilitating their establishment and operation as an alternative for white students who in most instances are seeking to avoid desegregated public schools".

[15] In 1976 the Academy, along with the Saint James School, was named in a suit filed against United States Secretary of the Treasury William Simon and Commissioner of Internal Revenue Donald C. Alexander by five women from Montgomery charging that the two men had encouraged the development of segregated schools by allowing them tax-deductible status.

[16] The school was identified as a discriminatory institution by the plaintiffs in Allen v. Wright, a lawsuit by black parents that was decided in 1984 by the U.S. Supreme Court.

[19] In June 2020, during the protests that followed the murder of George Floyd, headmaster John McWilliams said, "We must be willing to confront the uncomfortable fact that The Montgomery Academy, like many other independent schools founded in the South during the late 1950s, was not immune to the divisive forces of racism that shaped this city and community over the course of its history".

[20][15] The Montgomery Academy's first home was in a historic mansion, built in 1906, and serving as the official residence of Alabama's governor between 1911 and 1950 which was torn down to make way for Interstate 85.

The Perry Hill Road Campus for the Lower School, which by that time included "Form K" (Kindergarten), was opened in the late 1980s.

The firm was then later contracted to design a new building, the Mary Katherine Archibald Blount Upper School, as well as a pedestrian bridge connecting the academic campus with newly built athletic fields across the busy Vaughn Road.

In the summer of 2007, the school began a renovation, completed in 2009, of the old Mead Hall, which includes James W. Wilson Jr. Theater, as well as facilities for the forensics and drama programs.