They traditionally lived about 50 miles (80 km) inland and 50 miles (80 km) north of the modern day U.S.-Mexico border in the Peninsular Range of Southern California. Today their descendants are members of the federally recognized tribes known as the Pala Band of Luiseno Mission Indians, Morongo Band of Cahuilla Mission Indians, and Los Coyotes Band of Cahuilla and Cupeno Indians.
Several different groups combined to form Cupeño culture around 1000 to 1200 AD. They were closely related to Cahuilla culture. The Cupeño people traditionally lived in the mountains in the San Jose Valley at the headwaters of the San Luis Rey River. They lived in two autonomous villages, Wilákalpa and Kúpa, also spelled Cupa, located north of present-day Warner Springs, California. They also lived at Agua Caliente, located east of Lake Henshaw in an area crossed by State Highway 79 near Warner Springs. The 200-acre (0.81 km2) Cupeño Indian village site is now abandoned but evidence of its historical importance remains.
Spaniards entered Cupeño lands in 1795 and took control of the lands by the 19th century. After Mexico achieved independence, its government granted Juan Jose Warner, a naturalized American-Mexican citizen, nearly 45,000 acres (180 km2) of the land on November 28, 1844. Warner, like most other large landholders in California at the time, depended primarily on Indian labor. The villagers of Kúpa provided most of Warner's workforce on his cattle ranch. The Cupeño continued to reside at what the Spanish called Agua Caliente after the American occupation of California in 1847 to 1848, during the Mexican-American War. They built an adobe ranch house in 1849 and barn in 1857, which are still standing.
According to Julio Ortega, one of the oldest members of the Cupeño tribe, Warner set aside about 16 miles (26 km) of land surrounding the hot springs as the private domain of the Indians. Warner encouraged the Cupeño to construct a stone fence around their village and to keep their livestock separated from that of the ranch. Ortega felt that if the village had created its own boundaries, the Cupeño would still live there today. In observing the Cupeño's living conditions in 1846, W. H. Emory, brevet major with the United States Army Corps of Engineers, described the Indians as being held in a state of serfdom by Warner, and as being ill-treated. In 1849, Warner was arrested by the American forces for consorting with the Mexican government and was taken to Los Angeles.
In 1851, because of several issues of conflict, Antonio Garra, a Cupeño from Warner's Ranch, tried to organize a coalition of various Southern California Indian tribes to drive out all of the European Americans. His Garra Revolt failed, and settlers executed Garra. The Cupeño had attacked Warner and his ranch, burning some buildings. They lost structures at their settlement of Kúpa, too. Warner sent his family to Los Angeles, but continued to operate the ranch through others.