Manuel Antunes was born near the town of Sertã, into a family of poor economic and cultural resources. Both his parents were illiterate: his father, José Agostinho Antunes, worked as a farm hand and his mother, Maria de Jesus, was a housewife. Nevertheless, both their firstborn, Manuel, and their second son, José Antunes (1921-1997), completed higher education through the Society of Jesus. José left the seminary and completed his law degree as a worker-student, excelling in local life as a politician and educator to become mayor of the municipality of Sertã (1962-1974). When interviewed on her older brother's trajectory, the couple’s last child, Maria do Céu Antunes (b. 1924), referred to how his intelligence and drive to study had clashed with the socioeconomic reality of the household: following his brilliant performance at the elementary school in Sertã, he had attained the "best exam" classification in the fourth grade, but on learning of this result Manuel had been "sad" because "he had been the only child to go there barefoot.” Under these circumstances, "on the day of his first communion, Father José Lérias" - a local parish priest who had joined the Society of Jesus - asked the child "if he would like to become a priest and be able to study", to which he "immediately answered yes". The family budget was so tight that they could not afford the clothes he needed to join the seminary, and the money was raised thanks to “the congregation of a few Sisters of Mary who had heard about his predicament". (Biography…, 2011, pp 26-27, 157).

Manuel Antunes completed his lay education at the age of twelve. From then on, the future priest attended only institutions of the Society of Jesus, following a study plan equivalent to the secondary and higher education curricula, which in the Order of Saint Ignatius of Loyola revolved around cycles of humanistic-scientific and spiritual preparation. It took him two decades to be ordained to the priesthood and fifteen years had elapsed since entering the Novitiate.  

Between 1931 and 1936, despite several health setbacks, he completed his primary education at the Escola Apostólica [Apostolic School] (Seminário Menor [Junior Seminary]), first at the Seminário da Costa in Guimarães and later at Macieira de Cambra, before proceeding to the Postulancy. At 18, he entered the Novitiate, moving to the Convento de Alpendurada [Convent of Alpendurada] in Entre-os-Rios (Marco de Canaveses) for the two years of intensive preparatory initiation in order to enter the Order. In 1938, he progressed to the Juniorate, a cycle of intellectual preparation, normally lasting three years, beginning with two years of studies in Humanities, which the future priest completed in just one year. In the first year, which was taken at the Convento da Costa (Guimarães), Manuel Antunes' Portuguese Literature teacher was Father Lúcio Craveiro.

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