On 9th January, 1740, Junipero Serra was officially commissioned to teach philosophy for the next three years in the Convent of San Francisco. Two of his first students were Crespi and Francisco Palóu.
Junipero Serra desired to become a missionary in New Spain. He told Palóu: "The rumour is true. I am the one who intends to make this long journey, and I have been sorrowful because I would have no companion for so long a journey; but I would not on that account turn back from my purpose... In my heart I felt that inclination to speak to you as I was led to believe you would be interested." Palóu agreed and they both decided to volunteer to become missionaries. Juan Crespi also agreed to join them.
On 13th April 1749 the three men left the Convent of San Francisco and began their journey to Cádiz. The Board of Trade decided to document the physical characteristics of the missionaries. Crespi was described as: "twenty-eight years old, short of stature, sallow skin but somewhat florid complexion, blue eyes and dark hair."
Juan Crespi arrived at Vera Cruz in New Spain on 6th December, 1749. The voyage took ninety-nine days. Junipero Serra noted that he had not been seasick once. On arrival, Francisco Palóu recalls that Serra "delivered a sermon that eloquently spiritualized the entire voyage, emphasizing the protecting mantle of God's providence".
Carlos Francisco de Croix suggested to Carlos III that the Franciscans should attend to the people of Baja California. It was also agreed that the missionaries should push on quickly into Alta California in order to build a chain of missions that would stop other countries to try and colonise this territory. When asked to organise this campaign, the College of San Fernando de Mexico unanimously selected Junipero Serra, to carry out this task. Serra became president of these missions and Francisco Palóu was appointed as his deputy.
On 14th March, 1768, Serra, Crespi, and 14 missionaries left the port of San Blas on the small ship, Concepcion. The missionaries reached Loreto, two hundred miles up the east coast of Baja California on 1st April. They received a warm welcome from Gaspar de Portolà, who had been told to work closely with the missionaries.
Inspector General José de Gálvez had been sent to New Spain with orders to organize the settlement of Alta California. Gálvez began to arrange what became known as the "Sacred Expedition". It was decided that three ships, the San Carlos, the San Antonio, and the San José, should sail to San Diego Bay. It was also agreed to send two parties to make an overland journey from the Baja to Alta California.
The first ship, the San Carlos, sailed from La Paz on 10th January, 1769. The other two ships left on 15th February. The first overland party, led by Fernando Rivera Moncada, left from the Misión San Fernando Rey de España de Velicatá on 24th March. With him was Crespi, who had been given the task of recording details of the trip. Also in the party were 25 soldiers, and 42 Baju Christian Indians.
Rivera, Crespi, and the rest of his party reached San Diego on 14th May. They built a camp and waited for the others to arrive. The San Antonio, reached its destination in fifty-four days. The San Carlos took twice that time and the San José was lost with all aboard. The seaman on the ships suffered from scurvy and large numbers had died on the journey.
On 28th June, the overland party, that included Gaspar de Portolà and Junipero Serra arrived in San Diego. Serra later recalled: "It was a day of great rejoicing and merriment for all, because although each one in his respective journey had undergone the same hardships, their meeting through their mutual alleviation from hardship now became the material for mutual accounts of their experiences. And although this sort of consolation appears to be the solace of the miserable, for us it was the source of happiness. Thus was our arrival in health and happiness and contentment at the famous and desired Port of San Diego."
The following month Crespi joined an expedition that included Gaspar de Portolà, Fernando Rivera Moncada, José Francisco Ortega, Pedro Fages, sixty-three soldiers and a hundred mules loaded down with provisions, headed north on 14th July, 1769. Portolà reached the site of present day Los Angeles on 2nd August. The following day, they marched to what is now known as Santa Monica. Later that month they arrived at what became Santa Barbara, Portolà's party walked across the Santa Lucia Mountains to reach the mouth of the Salinas River. The fog obscured the shore and they therefore missed reaching Monterey Bay. The men had walked over a thousand miles from Misión San Fernando Rey de España de Velicatá.
Gaspar de Portolà and his men reached the San Francisco Bay area on 31st October. It has been claimed that José Francisco Ortega, his chief scout, was the first European to see the bay. He explored and named many localities in the region. Running short of provisions and forced to live on mule meat, they decided to return to San Diego to replenish supplies. The men arrived back on 24th January, 1770, remarkably, every member of the expedition had survived. Portolà and Juan Crespi had recorded the places they had stayed, the tribes they had met, possible mission sites, and the animals and wildflowers found.
Inspector General José de Gálvez had sent orders that their next task was to locate Monterey Bay. On 16th April, 1770, Junipero Serra, left the San Diego harbour on the San Antonio. The following day, Portolà's land expedition, that included Crespi and Pedro Fages marched north. José Francisco Ortega was left in charge of the Mission San Diego de Alcalá.
On 8th July, 1771 Serra and Crespi left Monterey with seven soldiers, three sailors and a few Baju Christian Indians, for the Sierra de Santa Lucia. Five days later he found a site for Mission San Antonio de Padua. The local Indians showed friendship by bringing seeds and acorns. Serra reciprocated with strings of beads and food made from corn and beans. Serra left Miguel Pieras and Buenaventura Sitjar in charge of the mission and returned to Monterey.
In 1772 Crespi made a sea journey to San Francisco with Pedro Fages. Crespi later described what happened when they arrived at San Pablo Bay: "When we arrived at this place there came to us eight Indians bringing as gifts wild seeds, as the others had done; in front, an Indian dancing, with a great bunch of feathers on his head, a pipe in his mouth, in one hand a banner of feathers, and a net. These things they presented to the captain. We gave them glass beads. They stayed with us quite a while and went back well content. They are very peaceable and agreeable, and it pleased us greatly that with their beards and light colouring they looked like Spaniards."
After making a full investigation of the area Crespi reported back that without finding a good overland route to San Francisco it would be difficult to establish a mission in the area: "From all that has been seen and learned, it follows that if the new mission should be established at the harbour itself or in its near vicinity, its animals and supplies could not come to it or be brought to it by land; nor, once it were founded, could there be any communication between it and this mission of Monterey or any others that may be founded in this direction, unless a pair of good longboats are supplied, with sailors, for getting persons from one side to the other."
Junipero Serra had a difficult relationship with Pedro Fages, the commander of Monterey. He was also disliked by his troops. One soldier wrote that: "The commandante used to beat us with cudgels; he would force us to buy from him at three times their value, the figs and raisins in which he was trading; he would make sick men go and cut down trees in the rain and would deprive them of their supper, if they protested; he would put us all on half rations even though food might be rotting in the storehouse. We had to live on rats, coyotes, vipers, crows, and generally every creature that moved on the earth, except beetles, to keep from starvation. We almost all became herbivorous, eating raw grass like our horses. How many times we wished we were six feet under ground."
Serra decided to visit Antonio María de Bucareli, the new viceroy of New Spain, in Mexico City. He left in October 1772, with his servant, Juan Evangelista. He did not arrive at the College of San Fernando de Mexico on 6th February, 1773. Bucareli asked Serra to put all his requests in writing. He gave the viceroy this document on 13th March. It was in fact a "Bill of Rights" for the Native Americans.
Serra also asked for the removal of Pedro Fages. Bucareli granted the request. He later commented: "The dispute with Don Pedro Fages... compelled Father Fray Junipero Serra almost in a dying condition to come to this capital to present his requests and to inform me personally a thing which rarely can be presented with such persuasion in writing. On his arrival I listened to him with the greatest pleasure and I realized the apostolic zeal that animated him while I accepted from his ideas those measures which appeared proper to me to carry out."
Don Denevi, the author of Junipero Serra (1985), has argued: Serra could reflect on a number of achievements: the promise of expeditions to explore and open up overland routes from Sonora and new Mexico; the separate marking of mission and military goods; the removal of immoral soldiers from the missions at the padres' request; the regulation of prices and standardization of weights; the recruiting of Mexicans on sailors' pay to the missions' fields; the protection of the padres' mail from tampering by military commanders; the provision of a doctor, blacksmiths, and carpenters, and of bells and vestments for the new missions; serious consideration of the shortage of mules; and pardons for all deserters."
On 24th January 1774, Junipero Serra took 97 people from San Blas on the Santiago to Monterey. This included two doctors, three blacksmiths, and two carpenters, some with wives and children. This was as a result of the arrangement reached with . Serra believed this would enable him to build a permanent Spanish community in this part of California. Serra left at San Diego and walked the rest of the journey to Monterey so that he could see for himself the progress that his missions were making. This included visits to the missions at San Diego de Alcalá, San Gabriel Arcangel, San Luis Obispo de Tolosa and San Antonio de Padua.
Serra arrived back at Mission San Carlos de Borromeo on 11th May, 1774. He was greeted warmly by Crespi and Francisco Palóu who were now both stationed in Monterey. When he left, there had been twenty-two baptisms since the founding of the mission; on his return, the total was one hundred seventy four. Serra was extremely happy about the progress that had been made in his absence.
Junipero Serra explained that: "Every day Indians are coming in from distant homes in the Sierra... They tell the padres they would like them to come to their territory. They see our church which stands before their eyes so neatly; they see the milpas with corn which are pretty to behold; they see so many children as well as people like themselves going about clothed who sing and eat well and work." Serra wrote that he was especially pleased with the impact the missionaries were having on the children: "The spectacle of seeing about a hundred young children of about the same age praying and answering individually all the questions asked on Christian doctrine, hearing them sing, seeing them going about clothed in cotton and woolen garments, playing happily and who deal with the padres so intimately as if they had always known them."
Antonio María de Bucareli selected Juan José Pérez Hernández to lead an expedition to explore the coast of the northwest. Crespi went along as his chaplain and diarist. The Santiago left Monterey on 11th June, 1774. The ship sailed as far north as Langara Island, one of the Queen Charlotte Islands. They were unable to go ashore and a lack of provisions and the poor health of his crew, meant that Pérez headed back to the Spanish settlement in Monterey, which he reached on 27th August.
According to Herbert E. Bolton, the editor of Francisco Palóu: Historical Memoirs of New California (1926): "Gentle character, devout Christian, zealous missionary, faithful companion, his peculiar fame will be that of diarist. Of all the men... so prolific in frontier extension up the Pacific Coast... Crespi alone participated in all the major path-breaking expeditions: from Velicatá to San Diego; from San Diego to San Francisco Bay; from Monterey to the San Joaquin Valley; from Monterey by sea to Alaska."
Crespi worked very closely with Junipero Serra in arranging the building of missions in California. The men came into conflict with Fernando Rivera Moncada, the commander of Monterey. The main problem was that Rivera did not share their passion for building new missions in the area. Serra wrote: "What are we doing here since it is plain that with this man in charge, no new missions will ever be established."
Serra and Crespi complained that the first mission south of San Carlos de Borromeo was San Antonio de Padua, nearly 70 miles away. Beyond was San Luis Obispo de Tolosa, another 75 miles to the south. The next mission was San Gabriel Arcangel, 212 miles away. The final mission, San Diego de Alcalá, was another 116 miles along the coast. Serra argued that these gaps needed filling in. He envisioned ten or eleven California missions being developed in his lifetime, "on a ladder with conveniently placed rungs". With missions founded at suitable intervals, travellers would spend only two or three days in the open between them.
Juan Bautista de Anza arrived in San Francisco on 28th March, 1776. Anza returned to Mexico and left behind José Joaquín Moraga to establish the Spanish settlement in the area. The Mission San Francisco de Asís, a log and thatch church was completed on 29th June, 1776. The mission was composed of adobe and redwood and was 144 feet long and 22 feet wide. Francisco Palóu was placed in charge of the mission that had been dedicated to San Francisco de Asis. The following year they established Mission Santa Clara de Asis.
In the summer of 1777 Crespi and Serra visited the two new missions. Afterwards Serra wrote: "Thanks be to God. Now Our Father Saint Francis, the crossbearer in the procession of missions, has come to the final point of the mainland of California; for in order to go farther, ships will be necessary."
In November 1781, Crespi was with Serra on a journey to Carmel. Serra was badly injured when his mule threw him to the ground. Crespi brought a doctor from San Jose, but despite the pain, it appeared that he had not broken any bones.
Juan Crespi was taken ill when he arrived back in Monterey. Serra described "his infirmities as chest trouble and a swelling of the legs that began in the lower extremities and gradually rose higher". The missionaries consulted their medical books but the remedies were ineffective and he died on 1st January, 1782.