On 19th October 1697, Father Juan María de Salvatierra disembarked with a few soldiers at the Bay of San Dionisio. At their arrival, they built a very simple shelter in front of which they placed a wooden cross. On 25th October, during a solemn procession, they brought the picture of our Lady of Loreto to this small chapel. This act marked the foundation of the mission and the land was declared property of the Spanish Crown. The mission of our Lady of Loreto Conchó was the first successful mission in both Baja and Alta California. It was baptized Head and mother of the missions in Baja and Alta California and constituted the starting point for the Jesuit evangelization of the peninsula. 
After the banning of the Jesuit Order in 1768, the mission remained in hands of the Franciscans.

Nowadays the mission church is located in the city centre of Loreto.