Work was begun on "The Great Stone Church" (the only chapel building in Alta California not constructed out of adobe) on February 2, 1797.
It was laid out in the shape of a cross, measuring 180 feet (55 m) long by 40 feet (12 m) wide with 50-foot (15 m) high walls, and included a 120-foot (37 m) tall campanile (bell tower) located adjacent to the main entrance.
Local legend has it that the tower could be seen for ten miles (16 km) or more, and that the bells could be heard from even farther away.
The sandstone building sat on a foundation seven feet thick.
Construction efforts required the participation of the entire neophyte population.
Stones were quarried from gullies and creek beds up to six miles (9.7 km) away and transported in carts (carretas) drawn by oxen, carried by hand, and even dragged to the building site.
Limestone was crushed into a powder on the Mission grounds to create a mortar that was more erosion-resistant than the actual stones.

On the afternoon of November 22, 1800, tremors from the 6.5-magnitude San Diego earthquake cracked the walls of the rising edifice, necessitating that repair work be performed.
Unfortunately, Señor Aguilár died six years into the project; his work was carried on by the priests and their charges, who made their best attempts to emulate the existing construction.
Lacking the skills of a master mason, however, led to irregular walls and necessitated the addition of a seventh roof dome.
The church was finally completed in 1806, and blessed by Fray Estévan Tapís on the evening of September 7; a two-day-long fiesta followed.
The sanctuary floors were paved with diamond-shaped tiles, and brick-lined niches displayed the statues of various saints.
It was by all accounts the most magnificent in all of California and a three-day feast was held in celebration of this monumental achievement.

On the morning of December 8, 1812, the "Feast Day of the Immaculate Conception of the Blessed Virgin", a series of large earthquakes shook Southern California during the first Sunday service.
The 7.5-magnitude San Juan Capistrano earthquake racked the doors to the church, pinning them shut.
When the ground finally stopped shaking, the bulk of the nave had come crashing down, and the bell tower was completely obliterated.
Forty native worshipers who were attending Mass and two boys who had been ringing the bells in the tower were buried under the rubble and lost their lives, and were subsequently interred in the Mission cemetery.
This was the second major setback the outpost had suffered, and followed severe storms and flooding that had damaged Mission buildings and ruined crops earlier in the year.

The priests immediately resumed holding services in Serra's Church.
Within a year a brick campanario ("bell wall") had been erected between the ruins of the stone church and the Mission's first chapel to support the four bells salvaged from the rubble of the campanile.
As the transept, sanctuary (reredos), and sacristia (sacristy) were all left standing, an attempt was made to rebuild the stone church in 1815 which failed due to a lack of construction expertise (the latter is the only element that is completely intact today).
Consequently, all of the construction work undertaken at the Mission grounds thereafter was of a strictly utilitarian nature.
José Barona and Boscana oversaw the construction of a small infirmary (hospital) building (located just outside the northwestern corner of the quadrangle) in 1814, "for the convenience of the sick."
It is here that Juaneño medicine men used traditional methods to heal the sick and injured.
Archaeological excavations in 1937 and 1979 unearthed what are believed to be the building's foundations.
Work was begun on "The Great Stone Church" (the only chapel building in Alta California not constructed out of adobe) on February 2, 1797. It was laid out in the shape of a cross, measuring 180 feet (55 m) long by 40 feet (12 m) wide with 50-foot (15 m) high walls, and included a 120-foot (37 m) tall campanile (bell tower) located adjacent to the main entrance. Local legend has it that the tower could be seen for ten miles (16 km) or more, and that the bells could be heard from even farther away. The sandstone building sat on a foundation seven feet thick. Construction efforts required the participation of the entire neophyte population. Stones were quarried from gullies and creek beds up to six miles (9.7 km) away and transported in carts (carretas) drawn by oxen, carried by hand, and even dragged to the building site. Limestone was crushed into a powder on the Mission grounds to create a mortar that was more erosion-resistant than the actual stones. 
On the afternoon of November 22, 1800, tremors from the 6.5-magnitude San Diego earthquake cracked the walls of the rising edifice, necessitating that repair work be performed. Unfortunately, Señor Aguilár died six years into the project; his work was carried on by the priests and their charges, who made their best attempts to emulate the existing construction. Lacking the skills of a master mason, however, led to irregular walls and necessitated the addition of a seventh roof dome. The church was finally completed in 1806, and blessed by Fray Estévan Tapís on the evening of September 7; a two-day-long fiesta followed. The sanctuary floors were paved with diamond-shaped tiles, and brick-lined niches displayed the statues of various saints. It was by all accounts the most magnificent in all of California and a three-day feast was held in celebration of this monumental achievement. 
On the morning of December 8, 1812, the "Feast Day of the Immaculate Conception of the Blessed Virgin", a series of large earthquakes shook Southern California during the first Sunday service. The 7.5-magnitude San Juan Capistrano earthquake racked the doors to the church, pinning them shut. When the ground finally stopped shaking, the bulk of the nave had come crashing down, and the bell tower was completely obliterated. Forty native worshipers who were attending Mass and two boys who had been ringing the bells in the tower were buried under the rubble and lost their lives, and were subsequently interred in the Mission cemetery. This was the second major setback the outpost had suffered, and followed severe storms and flooding that had damaged Mission buildings and ruined crops earlier in the year.
The priests immediately resumed holding services in Serra's Church. Within a year a brick campanario ("bell wall") had been erected between the ruins of the stone church and the Mission's first chapel to support the four bells salvaged from the rubble of the campanile. As the transept, sanctuary (reredos), and sacristia (sacristy) were all left standing, an attempt was made to rebuild the stone church in 1815 which failed due to a lack of construction expertise (the latter is the only element that is completely intact today). Consequently, all of the construction work undertaken at the Mission grounds thereafter was of a strictly utilitarian nature. José Barona and Boscana oversaw the construction of a small infirmary (hospital) building (located just outside the northwestern corner of the quadrangle) in 1814, "for the convenience of the sick." It is here that Juaneño medicine men used traditional methods to heal the sick and injured. Archaeological excavations in 1937 and 1979 unearthed what are believed to be the building's foundations.
Mission San Juan Capistrano