He subsequently professed solemn vows and was ordained in 1622, after which he served for several years as an advisor, preacher, superior of a Jesuit residence, and other jobs in various places.

[2] From 1652 Bobola also worked as a country "missionary", in various locations of Lithuania: these included Polotsk, where he was probably stationed in 1655, and also Pinsk, (both now in Belarus).

On 16 May 1657, during the Khmelnytsky Uprising, he was captured in Pinsk, and then killed in the village of Janów (now Ivanava, Belarus), by the Cossacks of Bohdan Chmielnicki.

[2] Several descriptions of Bobola's death exist, with these invariably involving him being subjected to a variety of tortures before being killed: In contrast to the above, a Russian examination of Bobola's corpse in January 1923 found no traces of gross mechanical violence on the surviving parts of the corpse that could establish cause of death.

The whereabouts of the remains were not known to the Catholic authorities, and Pope Pius XI charged the Papal Famine Relief Mission in Russia, headed by American Jesuit Father Edmund A. Walsh, with the task of locating and "rescuing" them.