When Jesuit Superior GeneralWlodimir Ledochowski died in 1942, World War II was in full fury in Europe and Janssens was the Jesuit Provincial trying to keep his province intact. The Vicar General, Norbert de Boynes, was unable to call a General Congregation because of the war. Thus, in effect, de Boynes was in charge of the governance of the Society for three years. The war ended in August 1945 and de Boynes was finally able to convene a General Congregation – the 29th – between 6 September and 23 October 1946. Janssens, as Provincial of his province, went to Rome as a delegate. The Congregation was held under Spartan conditions and many of the necessities were provided by the delegates from countries less affected by the war than the countries of Europe. On 15 September, the 57-year-old Belgian Jean-Baptiste Janssens was elected Superior General of the Society Of Jesus.
Generalate
Because of his delicate health and the oppressiveness of the Roman air, a sizeable piece of property in the Alban Hills – southeast of Rome – was purchased as a retreat for the general and his curia. This property, well known in the area as Villa Cavalletti, became a place of retreat not only for the general and the curia but also for the other Jesuits of Rome. It was also used by professors and students of the Gregorian University who could manage to get away for a few days of peace. In his famous Instruction on the Social Apostolate, considered a milestone in the Society's road to commitment to the so-called "social question", Janssens challenged the Jesuit educational institutions. In bold language for those days, the general speaks of completely uprooting the spirit of "caste" among Jesuits and their students. They should not appear "to be allied with the rich and the capitalists". Those especially who labor in the educational ministry should manifest "an interest and concern for the proletariat that is equal to, or even greater than, that shown to the rich". One can imagine the impact of these words on the schools. Nevertheless, disaffection toward the colleges remained strong, especially among young Jesuits. In 1957, after eleven years in office, he summoned the 30th General Congregation to provide him with a vicar general. During the 6 September to 11 November session, the delegates elected CanadianJohn Swain to the position. In 1960, in a letter to those engaged in education, the general had to confront those who doubted whether the colleges were a ministry proper to the Society or who asserted that they were not in conformity with the spirit of St. Ignatius. Janssens took important steps for the restructuring of the educational apostolate. Both on the provincial and national levels he set up offices of general Prefects of Studies. In this way there was more coordination among the colleges, both province and nationwide, as well as closer international collaboration. He appointed visitors of the colleges in various countries and regions, for example, Spain and Latin America. National and regional educational associations were encouraged within the Society. Statutes were elaborated to guide the work of the Prefects of Studies. In 1960, the first international meeting of experts in the college apostolate was held in Rome for the purpose of formulating common criteria of inspiration and action. The work of education in the Society was taking on a corporate character. Pope John XXIII had convened the Second Vatican Council to begin in 1962 to deal with many of the same problems that plagued Janssens during his generalate, Janssens had called for a diversification of Jesuit ministries to include more direct service to the poor.
Final years
After 18 years and one month as Superior General, Janssens died at the age of 75 on 5 October 1964. His body was taken to the Jesuit vault at Campo Verano where most of the Jesuits who die in Rome are interred.