The Rev. Mallalieu entered the New England Annual Conference of the M.E. Church in 1858. He spent twenty-four years in the Pastorate, serving just two years as a Presiding Elder. He declined educational positions which were offered to him. The Rev. Mallalieu became favorably known to his denomination through able contributions to Methodist periodicals. He was also notable as a platform speaker at places like Chautauqua and elsewhere. He was also a valued friend of Bishop Gilbert Haven, appointed to prepare the Memorial of him for the General Conference of 1880. Rev. Mallalieu was a delegate to the General Conferences of 1872, and 1884 (when he was at the head of his delegation). He was thought of as "a practical wide-awake minister, [who] makes a good speech in a way that assures you he could preach a better sermon..."
The Rev. Mr. Willard Francis Mallalieu was elected to the Episcopacy by the 1884 General Conference of the Methodist Episcopal Church.