Hilary returned to the Krakow community, Poland in 1935, and was appointed professor of Dogmatic Theology and Church History at the institute of the Polish Carmelite Province. Four years later, in 1939 as world war threatened, he was appointed prior of the Krakow community. In September of the same year, the Gestapo, who had entered Poland, began arresting friars from the Krakow community. During one of these arrests, Father Hilary offered himself in the place of another friar, who was older and suffering sickness. He understood his act to be the duty of his role as prior of the community. After his arrest he was transferred between various concentration camps and ended up at Dachau.

  At Dachau, Hilary was joined by other Carmelites who had been arrested, among them, Titus Brandsma. Letters from the time mention a ceremony held in secrecy to celebrate the feast of Our Lady of Mount Carmel on 16 July 1942 by a group of imprisoned Carmelites. During the winter of 1945, a typhus epidemic struck the camp. Hilary, knowing that he would likely not survive, volunteered to care for those who were suffering the disease. After 21 days of ministering to the sick and dying, Hilary contracted typhus and died of the disease on 25 March 1945, shortly before the liberation of the concentration camp. Previous Carmelite Prior General, Joseph Chalmers, reflecting on the life of Bl Hilary, wrote: “Had it not been for his heroic death, he would probably have been forgotten, because he never stood out in extraordinary things. But with that strength that grows from a life of prayer, acting in the presence of the Lord – something very typical and genuine of Carmelite spirituality – he gave himself up for others with the same simplicity with which he lived a quiet, hardworking life.”