In 1868, DeKoven was elected Warden of Racine College (a boarding school affiliated with the Episcopal Church), where he remained until 1870, and then again from 1872 onwards. Racine College was a rigorous classical school designed to prepare young men for leadership in church and society; DeKoven shaped its curriculum and spiritual formation with a high-church ethos.

DeKoven's great significance came through his theological and ecclesiastical leadership during the ritualist controversy of the 1870s. During this period, the American Episcopal Church was divided over the propriety of ceremonial worship: bishops and clergy influenced by Protestant evangelical tradition opposed the use of vestments, incense, liturgical music, and ceremonial elements, viewing them as "popish" and contrary to American simplicity. Bishops influenced by the Anglo-Catholic revival (and by English Tractarian theology) defended ceremonial practice as historically continuous, theologically legitimate, and spiritually enriching.

At the General Convention of 1871, DeKoven rose to defend the theological and historical legitimacy of ceremonial worship. His speeches were learned, eloquent, and rhetorically powerful: he demonstrated from patristic sources, medieval liturgiology, and Anglican formularies that ritual had always been part of Christian worship; he argued that ritual rightly used served the glory of God and the sanctification of the people; and he insisted that the Church could not, in the name of "Protestant simplicity," abolish elements that were ancient, theologically significant, and spiritually beneficial.

DeKoven's speeches influenced enough bishops and clergy to prevent the adoption of strict anti-ritual canons. At subsequent conventions (especially 1874), when attempts to legislate against ceremonial practice arose again, DeKoven's theological arguments were cited by defenders of liturgical freedom. His speeches and writings on the theology of worship became authoritative texts within Anglican ritualism.

DeKoven himself was a candidate for the episcopate on two occasions: diocesan conventions nominated him for election as bishop, and he was elected. However, his consecration was blocked by the House of Bishops—those opposed to ritualism were unwilling to confirm his election. This rejection of his consecration, despite his election by diocesan convention and his obvious pastoral and theological qualifications, became a symbol of the broader ritualist controversy and of the limits placed on Anglo-Catholic vision in the American church.

During the 1870s, DeKoven's health began to decline. He continued his work as educator and spiritual guide but was increasingly limited by illness. He died on March 22, 1879, at age 47. His death was widely mourned, and his legacy as the great defender of liturgical catholicism became enshrined in American Anglican tradition.

DeKoven's published sermons, addresses to General Convention (preserved in convention records), and correspondence reveal a man of profound theological learning, pastoral sensitivity, and rhetorical power. He combined patristic scholarship with contemporary ecclesiastical acumen. His vision was not narrow ritualism but a comprehensive Anglo-Catholicism that took seriously both the apostolic tradition and the reformation principle of reformed practice.