The stained glass windows were typically donated by family members in memory of U.S. Navy personnel; commemorative ceiling and wall tablets were likewise dedicated to various individuals and groups.

[5]: 6 "That the chaplain and his friends have been successful is attested by the many who come almost daily and sit for an hour in the chapel studying the works of art and receiving the spiritual uplift..."[10] The chapel served the Mare Island community — Naval and Marine officers, enlisted men and women, as well as the civilian workforce — much like a local community church, given how isolated and self-contained Mare Island was then.

As historian McDonald noted, "The chapel, more than any other building, bears witness to the closeness of the community that developed at the Mare Island Naval Shipyard.

As it was for numerous decades, the last scheduled service at St. Peter's Chapel ended with the singing of the Navy hymn, Eternal Father, Strong to Save.

Donated during the period from 1905 to 1930, typically in memory of U.S. Navy personnel, these windows beautify the chapel as well as symbolize the community spirit with which it was built and maintained through the decades.

[5]: 12  [9] The large triptych stained glass window at the back of the nave near the main vestibule entrance, made by Ingerson & Glaser and unveiled in 1907, shows Simon, called Peter, a toiler of the sea for whom the chapel is named.

The large window on the right side of the sanctuary is a pastoral view of the Good Shepherd and is dedicated to Chaplain Adam McAlister, with the inscription: "To whose devotion to this Chapel the placing of many of its Memorials is due."

The 9-ft-round Rose window high above the altar in the sanctuary is the ascendant Christ and is dedicated to those "in the U.S. Navy and Marine Corps who served on the Pacific Ocean".

lt was dedicated, according to the Shipyard Commandant, Captain Thomas A. Kearney, on 2 July 1930, "as an outward expression of affectionate appreciation and esteem," with the inscription, “To the Women of the Navy and the Marine Corps.” [11]