After some time he was transferred to the Flathead Mission of St. Mary's on Bitterroot River, western Montana, where he remained until the mission was temporarily abandoned on account of the hostile Blackfoot Indians in 1850. In 1854, he assumed charge of the Sacred Heart Mission established by Father Nicholas Point among the Coeur d'Alenes (Skitswish) of Northern Idaho. Here he designed and supervised the building of a church. With its altar and beautiful statues, carved by himself, it was described by a traveller as "a credit to any civilized country". Isaac Stevens, Governor of Washington Territory, who saw it in 1855, says in his official report: "The church was designed by the superior of the mission, Father Ravalli, a man of skill as an architect and, undoubtedly, judging from his well-thumbed books, of various accomplishments". In the general outbreak led by Yakima in 1856-67 his influence was largely instrumental in holding the northern tribes quiet.
In 1866 Nicholas Congiato, superior of the Rocky Mountain missions, established the old Mission of St. Mary's on the Bitter Root, among the Flathead Indians, and among those appointed to the station was Father Ravalli, who had been with it at its abandonment sixteen years before. Here he remained until his death.
"Fifty years a Jesuit and forty years a missionary, one of the noblest men that ever laboured in the ranks of the Church in Montana, his fame stands very high in Montana, where a later generation knows more of him than even of Father de Smet." (Chittenden).