Cruz published many books, including CBCP Guidelines on Sexual Abuse and Misconduct: A Critique, and Call of the Laity.
Cruz was elected President of the Federation of Asian Bishops' Conferences and served from 1993–2000.
Libel cases were filed against him after he accused the Philippine Amusement and Gaming Corp. (PAGCOR) of using female staff to act like "guest relations officers (GROs)" during the 2004 birthday celebration of First Gentleman Jose Miguel Arroyo.
[2][3] On September 8, 2009, Pope Benedict XVI accepted the retirement of Archbishop Cruz and was effective on November 4, 2009 where he was succeeded by Socrates Villegas of the Diocese of Balanga.
[4][5] Cruz died from complications of multiple organ failure caused by COVID-19 on August 26, 2020, at age 85 during the COVID-19 pandemic in the Philippines.