When the Spanish arrived in the 1540s, the San Juan people were living at the present pueblo and at a more westerly pueblo. The appearance of Gaspar Castaño de Sosa in 1591 marked the first contact between the San Juans and non-Natives. In 1598, Juan de Oñate arrived in the area with settlers, founding the colony of New Mexico. Oñate carried on the process, already underway in nearby areas, of subjugating the local Indians, forcing them to pay taxes in crops, cotton, and work and opening the door for Catholic missionaries to attack their religion. The Spanish renamed the pueblo San Juan Bautista; it was also known as San Juan de los Caballeros. At the same time, they introduced such new crops as peaches, wheat, and peppers into the region. In 1620, a royal decree created civil offices at each pueblo; silver-headed canes, many of which remain in use today, symbolized the governor's authority.
Trade along the Santa Fe Trail began in 1821. The trader Samuel Eldodt opened a general store at San Juan in 1863. Until it burned down in 1973, it was the oldest continuously operated store in New Mexico and furthered San Juan's reputation as a trade center. By the 1880s and the arrival of railroads, the Pueblos were dependent on many American-made goods, and the Native manufacture of weaving and pottery declined and nearly died out.
At San Juan, a summer and a winter cacique, appointed for life, oversaw the pueblo. Society was divided into two groups, summer (associated with the Squash kiva) and winter (associated with the Turquoise kiva); membership in a group was patrilineal. These groups were further divided into more than thirty clans. A number of secret societies also existed. For instance, the warrior society was concerned with hunting, war, crops, fertility, and curing. Each society had its own dances and ritual paraphernalia. Numerous life cycle rites, as well as songs, crafts, and communal activities such as maintenance of irrigation canals and performing dances, also ensured that one spent one's life "becoming" a Tewa.
People of San Juan further classified themselves into three categories: ordinary earth people, youths, and made people (priests of eight separate priest-hoods, half of which admit women as full members). Similarly, their physical world was divided into three corresponding categories: Village, farmlands, and other nearby lowlands, accessible to all and particularly the woman's domain, were delineated by four shrines to ancestors. Hills, mesas, and washes, defined by four sacred mesas and in the spiritual charge of the "youths," were a mediating environment in spatial, social, sexual, spiritual, and even subsistence terms. Mountains, a male realm of hunting and religious pilgrimages, were in the charge of the made people.
San Juan Pueblo originally featured multistory apartment-style dwellings constructed of adobe (earth-and-straw) bricks, with pine beams across the roof that were covered with poles, brush, and plaster. Floors were of wood plank or packed earth. The roof of one level served as the floor of another. The levels were interconnected by ladders. As an aid to defense, the traditional design included no doors or windows; entry was through the roof. Pithouses, or kivas, served as ceremonial chambers and clubhouses. The village plaza, around which the church and all dwellings were clustered, was the spiritual center of the village, a place where all the balanced forces of the world came together.