The Cebolla Wilderness (62,800 acres) includes four former Wilderness Study Areas: Rimrock, Little Rimrock, Sand Canyon, and Pinyon. La Ventana, the second largest natural arch in New Mexico, is within the Cebolla Wilderness, just east of State Road 117. The area is characterized by pinyon-, juniper-, and ponderosa-covered sandstone mesas and canyons. Its rimrock country and vertical sandstone escarpments are prime raptor nesting habitat. Birds of prey in the area include golden eagles, red-tailed hawks, prairie falcons, and great horned owls. Peregrine falcons migrate through the area. Large mammals include mule deer, bear, coyote, badger, bobcat, fox, and an occasional mountain lion.

The Cebolla Wilderness contains nationally significant archeological sites in extremely high densities. Most of them belong to the prehistoric Pueblo Chacoan system or the related but more recent Acoma Culture Province, but range in age from PaleoIndian (10,000 years ago) to Historic. In addition, this area was an interface between the prehistoric Anasazi (Pueblo) culture to the north and the prehistoric Mogollon culture to the south. The Dittert Site (a thirty- to forty-room Chacoan outlier) is listed on the National Register of Historic Places. Other key cultural resource properties which are wholly or partially within the Cebolla Wilderness are the Pinole Site and the Citadel Site, two extremely large pueblos which belong to the Acoma Culture Province. The publicly-owned portion of the Pinole Site is in the Cebolla Wilderness, with the private portion being in the Breaks Management Unit. The Cebolla Wilderness also includes important areas of Native American religious and traditional cultural use.