1.Morning Star Institute of Theology, Kolkata, West Bengal
This institute was affiliated with the Faculty of Theology of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on February 05, 2019. The director of this institute is Fr K. Henry Jose, MSFS.
2. Pilar Theological Institute, Pilar, Goa
This institute renewed its affiliation with the Faculty of Theology of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on June 23, 2023. The director of this institute is Fr John Elias Bennet, SFX.
3.St Pius X Institute of Theology, Goregaon East, Mumbai
This institute renewed its affiliation with the Faculty of Theology of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on June 27, 2023. The director of this institute is Fr Andrew Aranha.
4. Good Shepherd Institute of Theology, Rachol, Goa
This institute was affiliated with the Faculty of Theology of Pontifical Athenaeum, Jnana Deepa, Institute of Philosophy and Theology, Pune on June 23, 2023. The director of this institute is Fr Nelson Sequeira.
Bethany Vedavijnana Peeth OIC, Ramwadi, Pune
The Director of this extension centre is Fr Mathew Jacob Thiruvalil.