Although the church at Amenia was organized in 1886, the Amenia Cemetery Association was not organized until January 10, 1888.

The land was donated by Eben Whitney Chaffee and contains four acres, with the Rush River forming three of its four sides.

The cemetery lots had been surveyed on August 20, 1887 and provision was made for the graves that were already there to remain where they were with only a few being moved to a new lots.

The biggest funeral service and burial procession was on October 22, 1892, for Eben W. Chaffee. Over 250 people attended the funeral and about 50 horse teams went the mile to the gravesite.

The base for E. W. Chaffee's monument was unloaded June 5, 1896. The monument itself arrived on two flat cars and it took two weeks to unload, haul, and set up the four blocks of stone.

The cottonwood trees were planted in the cemetery on May 31, 1893, and the Amenia Cemetery Association was incorporated on January 15, 1895. The lots were priced at $6, $5, $4, and $3, remaining unchanged into the mid-1970s.

In 1954, the leftover funds from the former Amenia Congregational Church, were transferred to the Amenia Cemetery Association.

The former Amenia Congregational Church building was purchased by the Trinity Lutheran Church, which was organized in the late-1930s. When this church closed in 1971, the steeple was saved and eventually installed in the cemetery as a gazebo, in memory of members of the Kramer family.

The most famous gravesite in the cemetery is that of Herbert Fuller Chaffee, who was a victim of the RMS Titanic on April 15, 1912. His body was lost at sea, but an impressive monument bears his name and fate at the Amenia Cemetery. His wife, Carrie, a survivor of the Titanic, was buried in the Amenia Cemetery following her death in 1931.

At present, the Amenia Cemetery Association is still active and is governed by a board.