Already holding a doctorate in law, Werner Becker began studying Catholic theology in 1926, was ordained as a priest in 1932, and started work as a student chaplain at the University of Marburg. In mid-1938 Werner Becker moved to Leipzig and joined the Oratory of Saint Philipp Neri, a community of priests at the Church of Our Lady in the Lindenau district. In November 1939, he took over from his arrested fellow community member Heinrich Kahlefeld as head of Leipzig’s university chaplaincy.
In October 1943, Becker had to step down for allegedly helping a Jewish medicine student, Else Seelenfreund, to go underground. He was accused of hiding her with an aunt in the Rhineland. To evade imminent arrest, Becker volunteered as a medical orderly for the Wehrmacht. He was released from a Russian prisoner-of-war camp in 1945 and returned to the oratory in Leipzig, where he continued his work as a university chaplain until 1961. From 1966 to 1976 he headed the Ecumenical Office.
As of 2019, a memorial plaque in Leipzig commemorates the three oratory priests Werner Becker, Theodor Gunkel, and Josef Gülden.