Thirteen days after he dedicated the mission at San José, Fr. Lasuén was at San Juan Bautista, where he performed a like ceremony and San Juan joined the growing chain of Franciscan establishments on June 24, 1797.
Within six months, San Juan was listed as containing an adobe church, a monastery, granary, barracks, guardhouse and even adobe houses for the neophytes. By 1800, there were over 500 Indians living at the mission. When an earthquake caused considerable damage in October of that year, the padres took advantage of the opportunity to enlarge the church, and add certain facilities while making the needed repairs. The Indian population continued to increase and in 1803 extensive plans were made for the building of another church. The construction work was preceded by an elaborate ceremony to which people from all over the province were invited. During the dedication, a story of the event was sealed in a bottle and placed within the cornerstone.
In 1808, a new padre named Fr. Arroyo de la Cuesta arrived, bringing with him a tremendous energy, learning and imagination. Instead of the usual long and narrow nave, Fr. de la Cuesta convinced the builders that a wide church of three naves would be an unusual asset to San Juan. When the church was completed in 1812, it was the largest in the province and the only structure of its kind ever built by the Franciscans in California.
While the work progressed on the church, the neophyte congregation for whom it was planned declined at a considerable rate. In 1805, the Indian population had stood at 1,100. By 1812, when the church was completed, death and desertions had reduced the number by more than half. The great new edifice dwarfed the attending congregations, and Padre de la Cuesta walled in the two rows of arches which separated the three naves of the church. Except for the area near the altar, the church interior then resembled other mission churches, with the two outside naves forming large, separate rooms.
In decorating and furnishing the church, however, the energetic Franciscan was not to be denied. He continually sought out needed religious articles with an appreciative eye for the finest workmanship available. In 1820 he hired Thomas Doak, an American carpenter who was gifted with a decorative talent, and embellished the interior walls. It was Doak, incidentally, who deserted his ship and came ashore at Monterey in 1816 to become the first American citizen to settle in California. He took Spanish citizenship, found permanent residence at San Juan Bautista, and married a daughter of José Castro.
In 1790, the Spanish began to show considerable interest in the lands to the east of El Camino Real. San José, San Juan Bautista and Soledad reflected this interest. The unfriendly Indians were no longer avoided and, in the ranks of the military, such names as Vallejo, Amador, Moraga and Peralta were prominently connected with Indian fighting. As supply bases, San José and San Juan Bautista were constantly visited by groups of soldiers under the leadership of one or more of these men. Fighting was not the only method of approaching the pagans for, among Franciscans, the idea of establishing other missions to the east was never discarded.
One of the most curious consequences of this missionary fervor was the Mission del Rio de los Santos Reyes, which never quite existed in fact. In 1831, a Boston stonemason, Caleb Merrill, arrived at Mission San Diego. His services were appreciated at once by the Franciscans, and it was not long before he was working at Carmel. A short time later, a missionary expedition arrived at San Juan Bautista leaving behind them a pile of adobe masonry which was still evident in the 1860’s.
In 1812, Fr. Estévan Tápis, who had been acting as father presidente of the missions since the death of Fr. Lasuén in 1803, retired from the office and joined Fr. de la Cuesta at San Juan Bautista. Like Fr. Durán, he had a special talent for music and it was he who did so much to develop choral singing among the neophytes. The use of colored notes to identify the various vocal parts on the sheet of music was apparently introduced by Fr. Tápis during his stay in San Juan. In the congenial surroundings of San Juan Bautista, the elderly Franciscan spent the last of his 71 years. He was widely mourned when he died in 1825.
Fr. de la Cuesta continued to relegate the affairs of San Juan Bautista until the mission passed into the hands of the Zacatecan Franciscans. He was a forceful and imaginative man with a richer background and education than the majority of his fellow friars. One of his pleasures was the practice of endowing his newborn charges with names borrowed from the past. In this connection, Alfred Robinson, the American hide dealer who visited San Juan, related that the place abounded in “infant Platos, Ciceros and Alexanders.”
Fr. de la Cuesta knew more than a dozen Indian languages, and could deliver his sermons in seven tongues. During his stay at San Juan Bautista, he wrote two important works one was a compendium of Indian phrases, and the other was an exhaustive study of the Mutsumi language which received scientific recognition in 1860. An English barrel organ was acquired in 1826 and this crank-operated music maker produced wonder and enjoyment for the neophytes. A number of legends grew around this marvelous instrument, one of which gave it unusual powers and linked it with the founding of the mission. After Fr. de la Cuesta turned the direction of the mission over to the Zacatecan arrival in 1833, he joined his own Franciscans at San Miguel where he remained until his death in 1840.
The Zacatecan period lasted a brief two years. In 1835, under the secularization act, the mission was reduced to a curacy of the second class, under a civil administrator, and its assets liquidated. In place of the Indian village, a little settlement of whites came into existence near the mission in which there were some 50 inhabitants by the end of 1839. The new pueblo became the town of San Juan Bautista, whose history is one of romance, stirring pioneer days and much bloodshed. Through all these turbulent times, kindly padres lived at the mission, as they do today, administering to the religious needs of the community. From the day of its founding, San Juan Bautista never lacked spiritual guide or pastor, and on November 19, 1859, President James Buchanan returned San Juan Bautista Mission to the Church.
The wooden tower which was built about 1860 and later duplicated in concrete has been a part of the mission for so long, that when its removal was announced early in 1950, the old residents of the area were genuinely fearful that the structure was being desecrated. The tower, which was not in harmony with the rest of the church, was added by a secular priest in order to make his own tasks a little easier. It permitted ringing of the church bells comfortably no matter what the weather and, since he could not afford to pay the wages of an attendant, his action reveals a practical, rather than an artistic nature. After the departure of the priest, the earthquake of 1906 did extensive damage to the church. Fortunately, the monastery was not affected and the new padre did his best to restore the church, although both of the damaged outside naves were abandoned.
Today the mission at San Juan Bautista faces a most remarkable plaza. On it are found a hotel, a stable and two adobe mansions, all identical to the appearance 100 years ago. The Plaza Hotel, with its wonderful barroom, the old Castro House, the wagons of the livery stable, and the clumsy and elaborate beds in the Zanetta house were acquired by the State in 1933, and they combine to give a vivid picture of California just prior to the Gold Rush Days. There are no false fronts or artful imitations. These are the actual buildings of the community which stood near the beautiful old mission.
During 1976-77 the earthquake damage to the mission church at San Juan Bautista was at last repaired. Both side naves are now open, and the campanario, or bell wall, was rebuilt.