According to one newspaper article, the Catholic Cemetery was begun in the 1850s with a donation of land by Joseph Ebner for a Catholic burial ground lying south of Market Street and extending south several blocks. ("Cemetery Now is 60 Years Old: Grandfather of Late Joseph Ebner Donated Ground for it in the Early Fifties," La Crosse Tribune 29 July 1910; special section, p.5.) Additional land to the north of the original cemetery was purchased in 1885, and a chapel was constructed in 1891. Grottos, flower beds, and a lagoon were some of the improvements made to the site. Another newspaper article cites the cemetery's first sexton, Erhard Reisinger, with building the grottoes and stations of the cross.

A mausoleum was planned in 1977 to provide above ground burial, and was completed in 1981. The old grottoes were razed to accommodate it. In an 1985 article, the cemetery caretaker said he buried approximately 200 people a year. (Hollnagel, Gayda. "Business Keeps Family Close to Heaven's Gate," La Crosse Tribune 10 Jan. 1995, p.A-1.)