In 1869 he went to the Vatican Council as secretary to Cardinal Hohenlohe, and took an active part in opposing the dogma of papal infallibility, notably by supplying the opposition bishops with historical and theological material. He left Rome before the council closed. "No German ecclesiastic of his age appears to have won for himself so unusual a repute as a theologian and to have held so important a position, as the trusted counsellor of the leading German cardinal at the Vatican Council. The path was fairly open before him to the highest advancement in the Church of Rome, yet he deliberately sacrificed all such hopes and placed himself in the van of a hard and doubtful struggle" (The Guardian, 1872, p. 1004).
Sentence of excommunication was passed on Friedrich in April 1871, but he refused to acknowledge it and was upheld by the Bavarian government. He continued to perform ecclesiastical functions and maintained his academic position, becoming ordinary professor in 1872. In 1882 he was transferred to the philosophical faculty as professor of history. By this time he had to some extent withdrawn from the advanced position which he at first occupied in organizing the Old Catholic Church, for he was not in agreement with its abolition of enforced celibacy.
Friedrich was a prolific writer; among his chief works are: