Flowing from the Side of Christ on the Cross was the grace of reconciliation between God and Man (Rom. 5:8-11). Thus, on the evening of the Resurrection Our Lord appeared to His Apostles and said,

Peace be with you. As the Father has sent me, so I send you. And when he had said this, he breathed on them and said to them, Receive the holy Spirit. Whose sins you forgive are forgiven them, and whose sins you retain are retained. (John 20:21-23)

Padre Pio's conformity to the Pascal Mystery of His Lord necessarily including the ministry of reconciliation (2 Cor 5:18-20), its fruit. Toward that end he dedicated many hours of the day to the confessional, both in the mornings and the afternoon.

According to the practice common then he heard the confessions of men and women separately. The men's confessions he would hear in the sacristy, essentially in the open with a portable grill, while the women's would be heard in the church in his confessional.

To this task he brought an advantage that few confessors have, the ability to read hearts. Padre Pio's charism enabled him to know when someone was being deceitful in confession or simply had forgotten a serious sin, perhaps through lack of an adequate examination of conscience. In such cases he was able to tel the penitent exactly what they did and when, as well as any relevant circumstances. This drew many hundreds a day to him, moved by the grace of sincere repentance and the knowledge that Padre Pio could guide them with the wisdom of God in the spiritual life.

He also drew those who did not believe in his gifts or who intended to test the Padre. These were invariably unmasked, often in harsh ways. In the end they often repented, made a sincere confession and renewed their lives, despite their initial intentions.