1983–2010: Priesthood

Santos was ordained priest on September 10, 1983, at the Manila Cathedral by Manila archbishop Jaime Sin.^[4]

During his 27-year stint as priest of the Archdiocese of Manila from September 10, 1983 to July 8, 2010, he became parochial vicar at the Immaculate Concepcion Parish in Pasig (1983–1986), Chaplain of Pasig Catholic College (1983–1987), Pastor at San Antonio Abad Church in Maybunga (1986–1987), Professor of Church History, Patrology and Homiletics at San Carlos Graduate School of Theology and Holy Apostles Senior Seminary in Makati, Guest Priest at the Our Lady of Peace in EDSA and Our Lady of the Pillar Parish in Pilar Village, Las Piñas (1990–1997), Prefect of Discipline of the Philosophy Department in San Carlos Seminary (1990–1992), Professor of Church History at San Carlos Seminary of Manila (1990–1995), Academic Dean of San Carlos Graduate School of Theology, Library Director of San Gabriel Reyes Memorial Library at the San Carlos Graduate School of Theology, Chief Archivist of Manila Archdiocesan Archives and Curator and Director of Manila Archdiocesan Museum (1992–1997), Guest Lectuere for Novices and Postulants of Saint Paul of Chartres at Antipolo Mother House (1992–1995), Consultor of Pontificia Commisione per i Beni Culturali della Cheisa in the Vatican (1995–2005), Vice-Rector and Oeconomus of Pontificio Collegio Filippino in Rome, Italy (1997–1999), Rector of Pontificio Collegio Filippino in Rome, Italy (2000–2010), and National Coordinator of the Italian Bishops' Conference for the pastoral care of Filipino migrants in Italy (2003).

After several years in the ministry serving the archdiocese, he was sent to Rome in 1987 for further studies and took up his licentiate in church history in Pontificia Universita Gregoriana. He has been Academic Dean of San Carlos Graduate School of Theology. He also became Rector of Pontificio Collegio Filippino in Rome.

In 2005, he became a member of Pontificio Comitato per i Congressi Eucaristici Internazionali in the Vatican. He has also written a number of books regarding historical interest published by the Archdiocese of Manila and regarding homilies, prayers, and spirituality published by St. Paul's (SSP).

2010–2023: Bishop of Balanga

Pope Benedict XVI named Santos as fourth bishop of Balanga on Holy Thursday of 2010 in April 1, 2010. He continued to hold the position as priest of the Archdiocese of Manila and rector of Pontificio Collegio Filippino while holding the position as bishop-elect until his installation as the diocese's bishop in July 8, 2010. As bishop-elect and one month before his installation as Bishop of Balanga, he received episcopal consecration on June 24, 2010.^[3]

Santos decreed the creation of five parishes, four diocesan shrines, and one minor basilica, national shrine and chapel were created during his term as bishop of the diocese, with Residencia Sacerdotal, Retirement Home for Priests (Our Lady of Guadalupe Chapel) in Taglesville, Balanga was built months after he became bishop of Balanga. He also designated old churches in Hermosa, Orani, Samal, Abucay, Balanga City, Pilar and Orion as seven pilgrim churches that thousands of pilgrims from other provinces visit, especially during the Lenten season.^[5] Aside from Residencia Sacerdotal, he also built the National Shrine of the Parish Church of Saint John Paul II in Roman Superhighway, Culis, Hermosa, Virgen Milagrosa College Seminary in Balanga, Residencia Sacerdotal Diocesan Retirement Homes, Cancelleria Diocesana de Balanga, the renovated Bahay Puso which is the Diocesan Home for the Aged, and the newly built Diocesan Clinica de San Jose.^[6]

He made two quinquennial visit ad limina in Rome on December 2, 2010 (five months after he was installed as bishop of Balanga) and May 20, 2019.

Changes to the Balanga Cathedral were made during under Santos' tenure which are the improvement of its patio and numerous vendors were discouraged within the cathedral's premises. Walls and fences outside the cathedral were changed in 2011. Pavement of the ground on the exterior was made from 2017 to 2018, and the belfry added the bricks in 2019.^[7] In 2020, the cathedral's roof were painted from green and white to red. The Cathedral Shrine's Rectory and Sacristy with its fence and patio were also built during his tenure. Months before his tenure as Bishop of Balanga ended on July 22, 2023, the cathedral's leftmost door was removed and replaced with a wall.

He founded a foundation named Ad Seminandum RCS 10 Foundation, Inc., with the name being a reference to his motto as the diocese's bishop (Ad Seminandum), initials (RCS), and 10 being the month number of his birthday (October which is the 10th month of the year) and part of a number of a year when he became Bishop of Balanga (2010). His motto is also used as the name of an award (Ad Seminandum Award - Bishop's Award). Santos also founded the Diocesis de Balanga Multi-Purpose Credit Cooperative, the Santeria Religious Store and Sower's Printing Press to foster a brighter future and improvement of life. To maintain its permanency, he formed the Obispado de Balanga Bahay Puso Foundation and Diocesan Schools of Bataan Educational Foundation, Inc.

Santos became a governing council member for Asia of the International Migration Commission, Vatican from 2015 to 2022.

From June 5, 2020, to June 4, 2023, he served as acting rector and parish priest of the diocesan shrine and parish of St. Nicholas Tolentino (Mariveles, Bataan) in a concurrent capacity. During his 3-year tenure as acting rector and parish priest of the parish church, he had five assistant priests or parochial vicars which are the priests of Sto. Niño Parish Church in Alas-Asin named Robert Laracas, Ponciano G. Balmes, Marvin Gomez, Gerald Cuenca, and Christopher Alday (with Alday was demoted from being parochial vicar or assistant to simply a substitute priest under Region L. Tenorio). As in charge of the parish church on an acting position in addition to being Bishop of Balanga, he had all the duties and responsibilities of a rector and parish priest, such as inviting other priests and designate substitute priests such as Jay Quicho, change the schedule of masses, and initiate changes on the parish church like the changing of its facade and a new church bell from Royal Bells Philippines.^[8][9]

He continued written a number of books regarding homilies, prayers, and spirituality published by St. Paul's (SSP). In addition to spiritual books, he also wrote about the Diocese of Balanga and its churches, and Bataan province where the diocese has jurisdiction with. Santos issued 40 pastoral prayers during the COVID-19 pandemic. These prayers, he said, are his love letters to the people, the voices of love to God.

During his last three months as Bishop of Balanga, he served as apostolic administrator of the diocese aside from being the diocese's bishop from May 24 to July 22, 2023, as a preparation and transition period for his transfer to Diocese of Antipolo on the said date of July 2023.

2023–present: Bishop of Antipolo

Pope Francis named Santos as the fifth Bishop of Antipolo on May 24, 2023. Santos then became the diocese's bishop on his installation on July 22, 2023 where he succeeded Francisco Mendoza de Leon who reached the retirement age of 75 which ended his 13 years, 3 months, and 21 days tenure as Bishop of Balanga, 7, 6, and 4 months after Pope Benedict XVI (who named Santos as the latter position on April 2010) died on December 31, 2022, a funeral of the said pope on January 5, 2023 and the death of a diocesan administrator of Balanga between his predecessor Socrates Villegas and Santos himself from November 4, 2009 to July 8, 2010 Victor Ocampo on March 16, 2023 respectively, and one day after the death of another former administrator Antonio S. Dumaual on July 21, 2023. The installation ceremony was led by the Papal Nuncio to the Philippines Archbishop Charles John Brown together with Jose Cardinal Advincula, Archbishop of Manila.^[10] Even after he became Bishop of Antipolo on July 22, 2023, his coat of arms as Bishop of Balanga continued to be used by the Diocese of Balanga (the diocese that he formerly headed) during sede vacante period serving as a placeholder while awaiting for the installation of his successor as the diocese's bishop and unveiling of the successor's coat of arms since the said date of July 2023, concurrently used with his arms as Bishop of Antipolo.

On October 2, 2023, Santos returned to Balanga, Bataan for an honorary doctorate in recognition of his “distinguished service” to the community and made an honorary Doctor of Education of the Bataan Peninsula State University (BPSU). The awarding was held during the BPSU commencement exercises at the Bataan People’s Center, Bataan Provincial Capitol Compound, Balanga.^[11][12]

Catholic Bishops Conference of the Philippines

Since December 1, 2011, Santos held various positions at Catholic Bishops Conference of the Philippines (CBCP), such as being a member of CBCP Migrants and Itinerant People and Chairman, Pontificio Collegio Filippino (2011–2013), Vice Chairman of CBCP Commission on the Pontificio Collegio Filipino (2013–2017), Chairman of CBCP Commission for the Pastoral Care of Migrants and Itinerant People (2013–2019), CBCP Central Luzon Regional Representative and Member, CBCP Committee for International Congresses (2015–2019), Board Member of CBCP Pension Plan Committee and Member, CBCP Commission on Prison Pastoral Care (2017–2019), CBCP Bishop Promoter of Stella Maris - Philippines, and Chairman of CBCP Commission on Pontificio Collegio Filippino (2019–present).

Philippine politics

Santos expressed opposition against RH bill like former president Gloria Macapagal Arroyo as he said that the prayer vigil started with the rosary and a mass against RH bill and then followed by the prayer rally that will accompany with the rally at the EDSA Shrine to be officiated by the city government of Balanga. He stated that there are conferences, seminars, and marches against the RH bill, with the goal of the “diocesan-wide campaign” is to protect the sanctity of human life and the family, he told CBCP News.^[13][14]

Like with his predecessor Socrates Villegas, he expressed opposition on the revival of Bataan Nuclear Power Plant (BNPP) as it will put the lives on the brink of danger and shadow of impending death, result in the disruption of ecosystem, cause the soil to be poisoned and no longer viable to be cultivated, and livelihood will be destroyed.^[15]

Santos is appreciated with President Rodrigo Duterte's first State of the Nation Address (SONA) as he found out that it is inspiring and encouraging. He said that the President is magnanimous and forgiving – he did not resort to finger-pointing and the sins of the past. He pointed out realistically the situation and offered concrete action. He also thanked the President for his concern for the welfare of overseas Filipino workers. Santos stated that he is grateful for the president's compassion and concern to Overseas Filipino Workers (OFW) as he plans a single office to attend to their needs and asking to continue to protect the well-being of the OFWs. He also criticized the administration as he stated on an interview with Radio Veritas that his presidency is a disappointment and disgrace to the country. He lamented how Duterte's supporters laughed at his violent threats. Presidential Spokesperson told the bishop that instead of lambasting the President, Santos should instead pray for the President, “the way we pray for the Bishop’s enlightenment, that PRRD may run the affairs of the country well instead of lambasting him."^[16][17]

Following the denial of the broadcast franchise application of ABS-CBN, Santos expressed that the network's shutdown is a great loss, an added suffering for Filipinos, and never bring healing. He sympathized to the network's more than 11,000 employees who risk losing their jobs.^[18]