While Alencherry was pursuing higher studies at Aluva he served also as vicar of the filial church at Periyarmugham in the Syro-Malabar Catholic Major Archeparchy of Ernakulam-Angamaly. After completion of studies at Aluva, Alencherry was appointed as assistant vicar at the Cathedral church of Changanacherry and Director of the Archdiocesan Faith Formation department. Thereafter he served three years as secretary of the Commission for Catechism of the Kerala Catholic Bishops' Council (KCBC).