As the meeting was underway, Germany invaded Poland, sparking the Second World War. In response to the news, the members of the Congress, which included student from Poland, Germany, France, Italy, China, India, and the United Sates gathered in prayer before the Blessed Sacrament at the National Shrine of the Immaculate Conception in Washington. As a result of the War, the charted ship for the European delegates was cancelled and hundreds of students were stranded in the United States. After several weeks, many of the students could find ways to return home, but some chose to stay and support the work of the movement throughout the Americas.

During the War, Pax Romana opened a temporary office in Washington, DC. There under the leadership Ed Kirchner and with the help of Fr. John Courtney Murry, SJ, the office helped strengthen the federations in the Americas and helped coordinate some war relief efforts. During the War, Rudi Salat (Germany), one of the leaders stranded in the Untied States, after the Congress played an important role in promoting and organizing the movement in Latin America.