In 1983, he was appointed lecturer at the Jaffray Theological College in Makassar, South Sulawesi and for three years he also taught courses for pastors in Kalimantan.
He took the initiative of establishing the Walter Post Theological College there, so that students would not have to go all the way to Makassar if they wanted to study for the ministry.
He graduated in 1995 with a thesis on the Wege Bage, a new religious movement led by Zakheus Pakage in his home district of Paniai.
The research of Benny Giay is focused on the role of religion and the Christian faith in Papuan society.
Giay sees the movement as a legitimate way to reconcile traditional culture and Christianity, though as a member of the evangelical KINGMI Papua Church, he is also critical of it.
In later publications Giay advocates a church that is active in the human rights movement, and which is a spokesperson for Papuans, who are victims of repression by the Indonesian security forces.
In the context of this project he has written several studies, like the biographies of Theys Eluay, Rev Herman Saud and of John Rumbiak.
[1] It aimed at a discussion on ways in which Papuans could have "an opportunity to handle their own affairs" whether through full independence, through wide-ranging autonomy within the Indonesian unitary state, or through the formation of a federal system in which the province of Irian Jaya (now the provinces of Papua and West-Papua) would enjoy substantial autonomy.
In July 2002 the local organisation for the defence of human rights ELSHAM, the churches and the PDP set up a Peace Task force, with Benny Giay as its head.
[3] In December 2011 he was in that capacity a member of a team of four Papuan church leaders that met President Susilo Bandang Yudhoyono to argue in favor of a dialogue between the Indonesian Government and the Papua people in the presence of a neutral observer.