1.Marymatha Institute of Philosophy, Trichur, Kerala
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on July 20, 2019. The director of this institute is Fr Siby Varghese Cheruthottil.
2.Good Shepherd Institute of Philosophy, Kannur, Kerala
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on July 05, 2023. The director of this institute is Fr Jinson Kottiyanickal.
3.Jnana Niketan Institute of Philosophy and Religion, Aluva, Kerala
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on July 05, 2023. The director of this institute is Fr Tomy Alumkalkarot.
4.Arulanandar Institute of Philosophy, Madurai, Tamil Nadu
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on July 13, 2023. The director of this institute is Fr C. Lourdu Xavier.
5.Calvary Institute of Philosophy and Religion, Thrissur, Kerala
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on September 14, 2023. The director of this institute is Fr Jaison Vadakkan.
6. St. Albert's Institute of Philosophy (SAIP), Ranchi, Jharkhand
This institute was affiliated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on June 20, 2024. The director of this institute is Dr Raju Felix Crasta.
1. St Joseph's Institute of Philosophy, Alwaye, Kerala
This institute was aggregated with the Faculty of Philosophy of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on August 05, 2024. The director of this institute is Dr Paul Komban.