The St. Peter was constructed and launched at small shipyard near New Baltimore, Michigan in 1868. The schooner was built by master shipbuilder Peter Perry who owned and sailed the ship for its two seasons of service. The St. Peter was named for its owner and for St. Peter the Apostle, the patron saint of Shipbuilders. The vessel was put immediately to work, in September of 1863 delivering three shipments of 30,000 barrel staves from New Baltimore to Buffalo, New York. In October the schooner carried 50 tons of coal from Buffalo, New York to Wyandotte, Michigan. A month later, the St. Peter delivered 115,890 board feet of lumber to Buffalo from Algonac, Michigan. On the return trip the ship brought 140 tons of coal to Port Huron, Michigan before winter layup.

The next season had St. Peter hauling salt from Oswego, New York, to Toledo, Ohio; Shingles from Alpena, Michigan to Cleveland, Ohio and cleared the same day for Erie, Pennsylvania. In August the schooner cleared Cleveland to fetch a cargo of lumber and returned on 4 September. On 20 November while carrying a cargo of 7,000 bushels of wheat from Toledo to Cleveland, St. Peter struck the reef on the east side of West Sister Island on the eastern side of Lake Erie. The schooner began rapidly filling with water. Captain Perry attempted to run the ship toward Green Island, but St. Peter sank in 25 feet of water coming to rest on its side. Over the winter, St. Peter's outfit washed ashore near Put-In-Bay, Ohio. In early April 1870, salvors went to work and within a few weeks the vessel was raised and towed into Sandusky Bay. St. Peter spent 1870 being repaired at the shipyard of John Oade's in Detriot. Where the vessel was thoroughly rebuilt, St. Peter received a new deck, deck beams, stanchions, hatched and railing.

Salvor P.L. Oxford sold the restored St. Peter for $4,000 and Detroit was the vessels new homeport and the ship was remeasured. St. Peter sailed to Alpena to collect a cargo of cedar posts for Detroit. Throughout the 1871 season the schooner hauled salt, coal, wheat and barrel staves. On 23 November while sailing through thick fog enroute to Detroit from Buffalo, St. Peter grounded on Oxford Point near Clay Banks on Lake Erie. St. Peter was pulled off by the tug Hector and sustained no serious damage. In 1873 the St. Peter was sold again and had its homeport shifted to Chicago, Illinois. While St. Peter was sailing to its new homeport, a storm blew over Lake Michigan on 29 May 1873. When the St. Peter arrived in Chicago the next morning it struck the schooner Cousin Mary. The St. Peter broke all its bobstays and the Cousin Mary sank at the pier. On 12 June the barge Hershel swung against the St. Peter as it was waiting in a slip upriver from the Chicago Lumber Market. St. Peter had its bulwarks stove in and several stanchions broken. The St. Peter started carrying oats, grain, and corn from Chicago to ports on the eastern side of the Great Lakes.
On 5 May 1874 the St. Peter was loaded with 8,000 bushels of wheat at Chicago bound for Buffalo. There was concern at the time was that the schooner was overloaded and there was media speculation that the actual amount was 10,000 bushels of wheat. After departing Chicago, the St. Peter encountered stormy weather while approximately 35 miles northeast of Milwaukee and began to leak. The crew was put to the pumps but even after several hours, they were not able to keep the water out. When the water reached three feet deep, the decision was made to abandon the ship. The crew left everything behind when they escaped to the yawl. After only five minutes of rowing from the schooner, the St. Peter pitched forward sank bow first, and disappeared beneath the waves. The crew rowed through the night and arrived at Milwaukee the next morning. They reported the loss and caught a ride back to Chicago on another vessel.
The wreck of the St. Peter is sunk in deep water in central Lake Michigan. Its intact hull sits upright and the deck, bulwarks, and railing remain intact. The bowsprit, head-rigging are extant, but the ship's mast, spars, and rigging were thrown to the port side of the ship. The cabin roof blew off from the pressure of the sinking, but fragments remain within the wreckage. The St. Peter was located during a bathymetry survey conducted by the National Oceanic and Atmospheric Administration's (NOAA's) Office of Coast Survey between 30 June and 23 August 2022. The wreck site was investigated by Wisconsin Historical Society Maritime archaeologists and ROV operator Crossmon Consulting using a remotely operated vehicle (ROV), equipped with multibeam imaging sonar and video cameras. The wreck had not been visited before outside of this survey.