His 1640 Orthodox Confession of the Catholic and Apostolic Eastern Church was the first comprehensive Orthodox catechism to be written in any language. He wrote it in an attempt to reduce the continuing spread of Roman Catholic dogma among the Orthodox population of the Polish-Lithuanian Commonwealth, and using his opponent's methods, he wrote it in the Western question-and-answer catechism form. It would go on to be republished throughout Europe in Greek, Latin, and German. It did have some questionable elements, including the introduction of a concept suspiciously like that of Purgatory (something that does not exist in Orthodox theology) and his treatment of baptism by affusion (the pouring of water on the head) as equivalent to baptism by immersion (Orthodox tradition favors the latter, and allows the former only in the case of extreme emergencies). After revisions, however, his catechism was approved by a Church Council in Iași in 1642, and by the Patriarchs of Constantinople, Jerusalem, Alexandria, and Antioch in 1643. Nonetheless, this has not stopped it from being criticized as "the most Latin document ever to be adopted by an official Council of the Orthodox Church" by Bishop Kallistos (Ware), and as a "Latin pseudo-morphosis of Orthodoxy" by the Russian theologian Fr. Georges Florovsky.
Mohyla's monumental 1646 Trebnyk was a systematization and reform of liturgical practice for the lands governed by the Kyiv Metroplia. Mohyla had worked on it throughout his life as a monk and bishop and its publication was completed only two weeks before his death. Going back to original Greek sources (some of which, by that time, were located in Western Europe), he corrected many of the deviations in ritual that had crept in during the period when there was no "legal" Orthodox hierarchy in the Polish-Lithuanian Commonwealth. In many ways, his Trebnyk achieved the same types of reforms that Patriarch Nikon of Moscow would undertake in his jurisdiction a decade later.
One of the more visible and persistent changes introduced by Mohyla was in the wording of the prayer of absolution during the Sacrament of Confession (or Repentance). Instead of the form still used today in the Greek Church ("May God...forgive you all things, through me a sinner, both in this world and in the world to come..."), Mohyla's text has "May our Lord and God, Jesus Christ, by the grace and compassion of His love for mankind, forgive you...all your transgressions; and I, an unworthy priest, through His power given onto me, forgive you and absolve you from all your sins..." This form of the absolution prayer would go on to be adopted by the Church of Moscow, and is still used today in Ukraine, Russia, and in Russian or Ukrainian influenced churches in the United States and elsewhere in the world.