Beginning in 1931, Harry Downie began restoring the mission and worked continuously on the project for the next 50 years.

It was first established as Mission San Carlos Borromeo in Monterey, California near the native village of Tamo on June 3, 1770, by Father Junípero Serra.

It was named for Carlo Borromeo, Archbishop of Milan, Italy, and was the site of the first Christian confirmation in Alta California.

[5] Pedro Fages, who served as military governor of Alta California from 1770 to 1774, kept his headquarters in the polity's capitol, at the Presidio of Monterey.

[22] The original building in Monterey continued to operate as the Royal Presidio's chapel and later became the current Cathedral of San Carlos Borromeo.

"Mission Carmel", as it came to be known, was Serra's favorite[23] and, because it was close to Monterey, the capital of Alta California, he chose it as his headquarters.

After Serra's death, Father Fermín Lasuén replaced the adobe structure with one built of stone quarried from the nearby Santa Lucia Mountains.

"[20] To improve baptismal rates, they sought to convert key members of the Esselen and Rumsen tribes, including chiefs.

[22] The Esselen and Ohlone Indians who lived near the mission were baptized and then forcibly relocated and conscripted as forced laborers.

Over the years about 900 Esselen were baptized and brought to the Two missions at Carmel Valley, Soledad, and San Antonio that surrounding their native land.

The government stipulated that half the mission lands should be awarded to the native people, but this purpose was never accomplished.

As required by the Land Act of 1851, Archbishop Joseph Sadoc Alemany filed a claim on February 19, 1853, on behalf of the Roman Catholic Church.

[31] When the Roman Catholic Church gained full control of the buildings on October 19, 1859, the mission was in ruins.

[24] In 1884 Father Angel Casanova was able to gather enough private funds to replace the roof on the chapel sufficient to preserve it until the 1930s.

In 1931 Monsignor Philip Scher hired master cabinet maker Henry John ("Harry") Downie who had an excellent reputation for restoring Spanish antiques.

Downie lived nearby in Carmel and worked almost daily for nearly 50 years to restore the mission, ancillary buildings, walls, and grounds.

He painstakingly researched the church's architecture and site, often relying on original Spanish sources, and gathered genuine artifacts from across California.

In 1943 he began restoration of a building that had been on the south side of the quadrangle, although nothing was left but the eroded adobe foundation and a few ruined walls.

[39][40] In addition to its activity as a place of worship, Mission Carmel also hosts concerts, art exhibits, lectures, and numerous other community events.

In 1986, then-pastor Monsignor Eamon MacMahon acquired a Casavant Frères organ with horizontal trumpets.

The most important artwork conserved during their initial work was the Deposition, a painting commissioned by Father Serra prior to his death.

[40] In 2012, the foundation began a $6.2 million capital project to restore the Basilica which had not been touched since 1937 and had been deemed unsafe by the California State Unreinforced Masonry Act.

The contractors installed additional wood and steel beams to reinforce and tie the roof structure together.

The project upgraded the radiant heating system and included construction of an Americans with Disabilities Act-compliant restroom.

[40] The Lost Padre Mines of the Carmel Mission have woven themselves into the tapestry of local folklore, with their legacy recounted through various accounts, including those within Randall Reinstadt's notable works such as Ghosts, Bandits, and Legends of Old Monterey, Carmel and Surrounding Areas and Tales and Treasures of California Missions.

These narratives unveil a captivating history, suggesting that indigenous communities held knowledge of abundant gold deposits concealed within the untamed terrain of the Santa Lucia Mountains.

As whispers of these riches echoed through time, the enigmatic Lost Padre Mines became a testament to the allure of hidden treasures and the enduring mystique of the land.

It is plausible that this phenomenon can be attributed to some of the final descendants of the Mission Indians who resided and labored in the area.

[51][52][53] On September 27, 2015, in response to Serra's canonization, the San Carlos Borromeo de Carmelo Mission was vandalized.

The statue of Serra was toppled and splattered with paint, and the cemetery, the mission doors, a fountain, and a crucifix were as well.