Despite the story taking place in New Mexico, "Joe Kidd" was mostly shot within Arizona (per Republic World), in the area known as Old Tucson, a period-looking town that has served as the setting for a number of productions. The crew set their hearts on the southwestern state, wanting to take full advantage of its lush scenery. In particular, they wanted to capture the massive saguaro cactus, a plant only native to the Sonoran Desert, during the scenes taking place at Sinola County. Several onlookers in the area would also show up to watch the movie be filmed.
"Joe Kidd" would not be the first time the location appeared in a Western. The attractive desert environment has made Old Tucson Studios home to numerous other Westerns, including "Arizona," "Rio Bravo," "3:10 to Yuma," and "Gunfight at the O.K. Corral" (also directed by John Sturges). Other films outside the genre have also been shot there, including "Lilies of the Field," "Almost Famous," and Martin Scorsese's "Alice Doesn't Live Here Anymore" (via This is Tucson).
The rest of the film would be shot in various places in California. The Inyo National Forest was another significant location, receiving a credit in the film that reads, "Locations through the cooperation of The Forest Service USDA Inyo National Forest" (via AFI Catalog). Other California locations include Bishop and Lone Pine.