As patriarch, he received high Church honors from the Patriarchs of the Churches of [[Church of Antioch|Antioch]], [[Church of Jerusalem|Jerusalem]], [[Church of Alexandria|Alexandria]], [[Church of Russia|Russia]], [[Church of Greece|Greece]], [[Church of Bulgaria|Bulgaria]], [[Church of Romania|Romania]], and other Orthodox Churches.
Recognizing his work as a theologian and church historian, the [St. Vladimir's Orthodox Theological Seminary (Crestwood, New York)|St. Vladimir's Orthodox Theological Seminary]] in New York (in 1986), the Academy of Sciences in Crete (in 1997) and the [[St. Tikhon's Orthodox Theological Seminary (South Canaan, Pennsylvania)|St. Tikhon's Orthodox Theological Seminary]] in Pennsylvania (in 1998) conferred on him Honorary Doctorates of Theology.
Patr. Ilia II is an Honorary Academician of the Georgian Academy of Sciences (in 2003) and of the International Academy for the Promotion of Scientific Research (in 2007).