The youngest of the three children of Emiliano Villegas and Norma Buenaventura both from Pateros, he was born on September 28, 1960 when the town is still part of Rizal province.

He continued serve as rector of EDSA Shrine while being the diocese's bishop-elect from May 3 until he assumed office upon his installation as third bishop on July 3, 2004, ending the diocese's 10 months and 5 days sede vacante period or without a bishop in office under the diocesan administrator Antonio S. Dumaual and his 2 months bishop-elect period.

His installation ceremony or assumption into office as the diocese's third bishop was presided by the then-Archbishop of San Fernando, Pampanga Paciano Aniceto.

Samat Pilgrimage which is the diocese's annual event held on November or December of the year and is attended by thousands of young people from Bataan and different provinces in Luzon.

Donations came from several sources that included Mr. Daniel Meehan of the United States, two provinces, Netherlands and England, of the Sisters of Notre Dame.

On December 8, 2008, Clinica Diocesano de San Jose, the diocese's clinic, was founded which is a weekly medical and dental mission for the poor people of Bataan.

On August 5, 2009, Bishop Villegas, along with then-Manila Archbishop Cardinal Gaudencio Rosales, officiated at the Requiem Mass for former President of the Philippines Corazon Aquino held at the Manila Cathedral.

Villegas was then installed upon Cruz's retirement as the archdiocese's archbishop on November 4, 2009, ending his 5 years, 6 months, and 1 day tenure as third Bishop of Balanga.

He was succeeded by Ruperto Santos upon his appointment to the position as fourth Bishop of Balanga on April 1, 2010 and installed into office on July 8, 2010.

Jhoen Buenaventura on December 7, 2009, dedication of Stella Maris Retreat Center on January 10, 2010, and finally the installation of Santos into office on July 8, 2010.

Due to the sudden death of San Fernando de La Union Bishop Artemio Rillera, he became the Apostolic Administrator of the said vacant See from November 13, 2011 to January 19, 2013, in a concurrent capacity.

He was the Chairman of the Episcopal Commission for Catechesis and Catholic Education of the CBCP from 2003 until 2012 and formerly a member of the Presidential Committee of the Pontifical Council for the Family.

In August 2005, Villegas told Filipino Catholics that they "cannot participate in any way or even attend religious or legal ceremonies that celebrate and legitimize homosexual unions".

[7] Villegas' views on social and political issues in the Philippines have not been without controversy, mainly regarding high-profile issues such as the Reproductive Health Bill, the re-imposition of death penalty (long-opposed by the Catholic Church),[8] human rights violations, extrajudicial killings under the Duterte administration, and the burial of dictator Ferdinand Marcos at the Libingan ng mga Bayani (Heroes' Cemetery).

[19] Due to the non-renewal of broadcast franchise application of ABS-CBN, Villegas expressed that the network's issues could have been dealt in with proper proceedings and decried that shutting down from the airwaves, reminding the Philippine government of the importance of free press in a democratic country.

[20][21] In October 2023, Villegas publicly stated that the International Criminal Court investigators should be allowed to probe into allegations of human rights abuses in Duterte's war on drugs.