But one and a half months after that he was summoned to return, due to the start of World War II and he left the Army only after the defeat of the Belgian Armed Forces by the German occupiers.

In 1952 he defended and published his doctoral thesis at the Dominican school of theology Le Saulchoir: De sacramentele heilseconomie [The redeeming economy of the sacraments].

Due to his having been the "ghost writer" of the Dutch bishops' Pastoral Letter on the upcoming Council in 1961, he was rendered suspect with the Congregation of the Holy Office, led by Cardinal Alfredo Ottaviani (President) and the Dutchman Sebastiaan Tromp (Secretary).

These anonymous comments on the theological schemata debated at Vatican II, and the articles he published, also influenced the development of several conciliar constitutions such as Dei verbum and Lumen gentium.

Already in 1963, together with Chenu, Congar, Karl Rahner, and Hans Küng, he was involved in preparing the rise of the new theological journal Concilium, which was officially founded in 1965 with the support of Paul Brand and Antoine Van den Boogaard, and which promoted "reformist" thought.

[9] On the basis of his study of the earliest Christian sources – often drawing upon the exegetical insight of his Nijmegen colleague Bas van Iersel – Schillebeeckx confronted such debated questions as the position of priests, e.g., by supporting a proposal to disconnect sacramental priesthood and the obligation to celibacy.

At the sessions of this synod, the Dutch bishops, intellectuals, and representatives from many Catholic organisations tried to implement what they perceived as the major progressive objectives of the Second Vatican Council.

[10] The empty tomb was, in his opinion, an unnecessary hypothesis, since “an eschatological, bodily resurrection, theologically speaking, has nothing to do, however, with a corpse.”[11] That was merely a "crude and naive realism of what 'appearances of Jesus'" meant.

[12] Although the books were followed by a couple of articles where Schillebeeckx defends himself against criticism and tones down his radicalism, on 20 October 1976 the Congregation for the Doctrine of the Faith wrote to him with various objections.

The conclusions of the congregation, however, left the impression that a genuine accord had not been reached, and he continued to receive notifications from Church authorities for his repeated writings.

[13][14] His christology was criticized by Cardinal Franjo Šeper and then-Cardinal Joseph Ratzinger, whom Schillebeeckx already knew at the Second Vatican Council and who was later elected Pope Benedict XVI.

[6] In 1984 his orthodoxy was again called into question by the Congregation for the Doctrine of the Faith: he was summoned to Rome to explain his views expressed in The Ministry in the Church, which were regarded as Protestant.