The outbreak of World War I interrupted his education. After it ended, he decided to leave and connect his future with the clergy. He began his studies at the Salesian center for late vocations from the Czech Republic in Perosa Argentine, Italy. He was ordained a priest on July 1, 1932 and obtained his doctorate at the Gregorian University in Rome.

He returned to the Czech Republic, where he began to spread Salesian ideas, build education centers and churches, and also began to support, for example, a philosophical studentate (monastery) with a boarding school for Czechs and Slovaks. In the 1930s, the work of the priest Trochta was dynamic, thanks to the support of local communities and the help of the Czechoslovak authorities. However, at the end of the decade, Czechoslovakia, and soon all of Europe, fell into troubled times. Trochta’s homeland was annexed to Germany, and Slovakia was turned into a puppet state.

In Nazi Germany, not only Jews, Roma and homosexuals were persecuted. Clergy, including Catholic ones, also faced terror in the country. Himmler, Goebbels and Hans Frank mentioned combating the clergy. The later deputy protector of Bohemia and Moravia, Reinhard Heydrich, one of the organizers of the Wannsee conference, and therefore the perpetrators of the Holocaust, had hatred for various religious denominations and even issued orders to the Gestapo to deal with any manifestation of religious opposition. During the Nazi era, priests, nuns and monks were arrested, Catholic schools were closed, church property was appropriated, and Christian youth organizations were dissolved, including Salesian. Catholic priests were systematically repressed. In Dachau, a model concentration camp for other places of this type, there was a special, separate barracks (No. 26) for Catholic and Protestant clergy. There were held over 400 people.

Similar repressions fell on Czech cultural and religious centers. Nearly 500 priests and monks were locked up in concentration camps. On May 27, 1942, the Czech resistance movement assassinated Heydrich. A day later, revenge began in the occupied country with redoubled force of terror. The day after the attack, Štěpán Trochta was arrested and then sent to the Theresienstadt concentration camp. His “guilt” was contacts with the nunciature and secret contacts with Italy.

After a short time, the priest was sent to subsequent concentration camps, in Mauthausen and Dachau. Once he miraculously escaped death – he was called, along with 7 other prisoners, to work emptying latrines during roll call. While working, pushing a cart full of waste, Štěpán Trochta slipped in his wooden shoes. An impatient SS man shot him twice. The priest fell to the ground and pretended to be dead, hoping that the German would not come and kill him. The injured man was thrown onto a cart that transported the dead bodies to the crematorium. Lying among dead fellow prisoners, Štěpán Trochta lost consciousness. Fortunately for him, the prisoners did not take him to the place because the alarm sounded, ending his work and calling everyone to the evening roll call. Štěpán Trochta woke up, tore off a piece of clothing from one dead prisoner and bandaged himself, and went to the camp hospital.

Trochta lived to see his freedom in the Dachau camp, where his fellow prisoners remembered him as a person who always helped others, not only materially, but also spiritually, including: sharing food received from parcels and administering sacraments.

After the war he returned to Czechoslovakia. He was appointed bishop by Pope Pius XII, but he was soon repressed by the communist authorities, who interned him and then sentenced him to 25 years in prison. The amnested person worked as a builder. In 1962, he retired and lived in a nursing home under the supervision of the militia. He died in 1974.