John tried in his various apostolates to lead people from ignorance and superstition to the light of truth. He identified himself with the downtrodden and oppressed. He worked hard for the uplifting of the poor especially in an area - Chowannur - where the majority were Hindus and non Catholics. The last 28 years of his life (1928-1956) he worked in this area, with a brief interlude in Palayur (1940-1941). People used to call him Achan Thampuran (meaning lord priest) in respect and appreciation of the yeomen service he did for the people, especially the scheduled castes and other non Catholics. He prayed that he, together with the fellow priests, should strive to alleviate the sufferings of our poor pulayas and to ameliorate their condition, to bring them up to the equal social condition. In Chowannur and Kunnamkulam, Fr. Ukken also became a veritable model in interreligious dialogue and ecumenism.
The special charisms that he intended for his sisters were: caring of the sick, tending those who are in deathbed, uplifting the poor and giving catechetical formation. The sisters took family visits and counselling as an important facet of their apostolate. His advice to the sisters was: Your task is to love; let no one surpass you in love.
The Lights from Heaven, his spiritual diaries, show forth the inner saintliness of the person. His founding of the Congregation of the Sisters of Charity was a bold attempt to perpetuate the ideas of charity through a visible institution. His work among the poor, especially in the last phase of his life at Chowannur, basing himself on the ideals of the Gospel, is yet another dimension of his holiness.
John tried to acquire moral perfection by earnestly practising justice, and acting according to his well-formed conscience. He respected the elders and obeyed the superiors. His firm faith in Gods providence, thirst for reconciliation with him and the readiness to propagate the faith are all well testified from his spiritual diaries and are the hallmarks of his inner saintliness
Personally Fr. John lived a life of prayer and penance. The long hours he spent before the Eucharist were moments of his own personal sanctification and those of the community he served. For him, the Holy Mass was the chief event of the day. He saw Eucharist as the source of spiritual power against temptations. Fr. John routinely practised penance and mortification. He applied himself to rigorous fasting and an austere way of life. He was a model to his parishners and especially to the sisters in the virtue of heroic suffering by which he experienced the closeness with the crucified Lord. John himself was a good preacher and has preached retreats for priests a number of times. John was also filled with missionary spirit, which is evident from the fact that he sent many sisters to remote areas of Kerala.