The first cemetery at Saint John's (c.1869), a plot of about thirty square feet, was located in the area in front of the present Abbot Peter Engel Science Center.

In 1875, Wolfgang Northman, OSB, drew up plans for the layout of a new cemetery to be located on an acre of a hill lying a quarter mile south of the monastery. In the winter of 1875-76, Abbot Alexius Edelbrock, OSB, ordered that the hill be cleared of timber, and a worthy cemetery laid out on its eastern slope for the members of the community and the local parish of Saint John the Baptist. Ironically, Wolfgang died on February 8, 1876, at the age of 33, and was the first to be interred in the new cemetery. On February 10, following a solemn Requiem Mass, a procession lead by the mournful sounds of the Saint John's College Band, accompanied a large number of monks and mourners to the cemetery to bury Wolfgang.

On September 12, 1876, a large white cross was raised on the hill and on November 2, the monks buried in the original cemetery were re-interred: Demetrius de Marogna, OSB, the first prior of St. John's (†March 27, 1869); Placid Brixius, OSB, a carpenter who helped build the first convent for the Benedictine Sisters at St. Joseph (†June 28, 1871); and Othmar Wirtz, OSB, the prior who oversaw the move of the monastery from St. Cloud to Collegeville (†June 8, 1874). Three students from the college also were re-interred in the new cemetery: Max Schmoeger (†January 1, 1870); Martin McIntire (†March 4, 1871); and John Bonne (†April 7, 1872). Two monks who had been buried in the parish cemetery in St. Joseph, were re-interred on November 9, 1876: Benno Muckenthaler (†March 27, 1859), one of the pioneer monks whose relatives in Bavaria sent him the first church bell in Stearns County, and Novice Gall Kederly (†November 5, 1864). Benno and Gall died before the community was located at the present site and are considered monks of Saint Vincent's Archabbey, Latrobe, Pennsylvania.

Transporting the coffins of deceased monks to the cemetery in the early years was by an open surrey. In 1932 a horse-drawn hearse, equipped with side-lantern and heavy black curtains, was given to Saint John's by the Wenner Funeral Home of Cold Spring. For 21 years this stately carriage, pulled by two horses, transported the remains of over seventy monks to the cemetery. On July 22, 1953, following the funeral of Innocent Gertken, OSB, the hearse was retired and given to the St. Cloud Chamber of Commerce.