[citation needed] Nebres was also one of the founders of the consortium of the leading universities in Manila to develop Ph.D. programs in mathematics, physics and chemistry.

The consortium has succeeded in developing a critical mass of scientists in these areas, has developed extensive links with scientists abroad (particularly in Australia and Japan), and is now the core of a large network of schools in the Philippines (more than 110 high schools as well as over 30 colleges and universities) which are supported by the Philippines’ Department of Science and Technology as the leadership group for improving science and engineering education in the country.

His main concerns apart from the regular duties of a university president are the strengthening of basic education and of science and technology in the Philippines.

[citation needed] Nebres also worked to establish the Center for Community Services and the first conscientization and politicalization programs of the Ateneo de Manila in the 1970s.

He also helped in the political programs of various parties and groups during the years of forming alternatives to the Ferdinand Marcos martial law regime.

As Provincial Superior of the Jesuits in the Philippines from 1983 to 1989, much of his work was to support and coordinate efforts on the part of the Church in the years prior to and immediately after the People Power Revolution in 1986.

[citation needed] On September 4, 2007, the Presidential Task Force on Education under the Office of the President named Nebres, chairman.

Gloria Macapagal Arroyo signed Executive Order 635 on August 24 creating a presidential task force to assess, plan and monitor the entire educational system.

[5] On December 5, 2007, Nebres launched "Frontline Leadership," a book project of the Ateneo School of Government (sponsored by German foundation Konrad Adenauer Stiftung) was written by several authors.

His resignation on September 25, 2012, came in the wake of PLDT Chairman Manny Pangilinan's "disengagement" from the Ateneo due to "irreconcilable" differences of positions taken on controversial issues, particularly the Reproductive Health Bill in which the Catholic Church is against, and mining.

[citation needed] The Catholic Bishops Conference of the Philippines (CBCP) on June 15, 2008, stated that "Ateneo de Manila University president Bienvenido Nebres will be formally honored as among the DOST's "50 Men and Women of Science" July to September; the DOST Citation for Nebres described him as an "education icon," having reconciled the fields of science and religion with his work.