[2][3] Awad co-founded the society due to Muslims' concerns to "maintain their religion for themselves and to pass on their Islamic heritage to their children in the face of strong pressures toward assimilation.

[4] The society began with several families who met every Sunday at Shaffer Hall in the Homewood Campus of Johns Hopkins University to pray, discuss scriptures, and study Arabic.

[1][9] On March 7, 1982, 52-year-old Sunday school teacher and director of education Muhammad Aslam was shot and killed in his hometown of Philadelphia, from which he would regularly travel from to the Society.

[16] An open house was held at the society for the public on September 23,[17] which was attended by Baltimore mayor and future Maryland governor Martin O'Malley.

[21] On December 14, 2015, the White House held three meetings with Muslim leaders to discuss concerns about rising hostility toward religious minorities.

[22] A White House official stated that its purpose is "to celebrate the contributions Muslim Americans make to our nation and reaffirm the importance of religious freedom to our way of life".

The expansion planned to add a library, more classrooms, larger prayer areas for major events, and move the Al-Rahmah Quran Academy closer to the main building.

[4] In response to the COVID-19 pandemic, the Islamic Society of Baltimore cancelled all prayers and events, broadcasting programs and religious activities from its YouTube channel to reach people.

[19] The criticisms of the conservative media revolved around Mohammed Adam El-Sheikh, a former imam at the mosque, who was a member of the Muslim Brotherhood before cutting ties in 1992.

Coinciding with Obama's visit in 2016, this comment gained controversy among several right-wing media such as The Daily Caller,[19] Fox News,[14] and The Washington Times.

[20] ThinkProgress, however, commented that these "right-wing outlets omitted that fact that the quote was a specific reference to the uptick in violence between Israelis and Palestinians — not Americans — and that Sheikh immediately added that 'condemnation of indiscriminate killing of civilians' was widespread in his community.

[20] El-Sheikh was also a regional director for the Islamic American Relief Agency, whose parent organization has been cited by the U.S. Treasury Department for connections to Al-Qaeda and the Taliban.

[14][20] In 2011, Suleiman Anwar Bengharsa, a Muslim cleric, prison chaplain, and imam, was a volunteer guest speaker at the Islamic Society of Baltimore.

According to an FBI affidavit filed in federal court, in June 2015, he supplied $1,300 to Sebastian Gregerson in Detroit, who used it to expand his arsenal of firearms and grenades, although Bengharsa claimed it was intended for charity.