Before his election as Senator, he was appointed Minister, later Secretary of Justice (1986–1987) by then President Corazon C.

[2] During Martial Law, he was the one of its active critics from the opposition and lawyered for some political detainees including then Senator Ninoy Aquino.

For his outstanding achievements and contributions in the fields of law, education, and public service, he was conferred the degrees of Doctor of Laws, honoris causa, both by the University of Bohol and the University of Misamis (1987); Doctor of Public Administration, honoris causa, by the Polytechnic University of the Philippines (1991); and Doctor of Technology Education, honoris causa, by the Rizal Technological Colleges (1995).

After Gonzales' third and last term as Senate President and his term as a senator ended on June 30, 1998, Gonzales then entered the corporate world by becoming the President and Publisher of the Manila Bulletin and was elected as member of its governing Board of Directors.

Gonzales was married to Candida Medina for more than fifty years and was the father of four children: Myrna, Aida, Rhodora and Neptali II.

In recognition of his strong adherence to family values, he was presented with the "1994 ASEAN Father for Public Service Award" and the "1996 Ama ng Bayan Award" by the Golden Mother & Father Foundation and the "1996 Special Ideal Parents Award" from the Ideal Community Foundation of the Philippines and the Golden Mother & Father Foundation, and the "1996 Golden Parents Special Award" from the Golden Mother & Father Foundation.