In the opinion of a contemporary, the historian Manouil Gedeon, the new patriarch was characterized by a deep "zeal for the Church and austerity in his customs - but also by an unforgivable inflexibility in his own ideas" ("Τον Γρηγόριον ΣΤ' εχαρακτήριζε ζήλος υπέρ της Εκκλησίας, αυστηρότης εν τοις ηθεσιν, άλλ' ασύγγνωστος εμμονή εις πάσαν αυτόυ ιδέαν").

On 19 December 1839 he published a Patriarchal and Synodic newsletter («Περί της νεωστί αναφανείσης αντιχρίστου διδαλίας του Θεοσεβισμού») against Theophilos Kairis and his teaching.

The vigour of Gregory VI's efforts to insulate his flock, not only in the Ottoman Empire but also in the Kingdom of Greece and the United States of the Ionian Islands, from heterodox religious influences incurred the displeasure of all governments in the region during the late 1830s.

In 1839, these tensions came to a head when the patriarch issued an encyclical condemning various uncanonical changes to family law promulgated by the British colonial authorities on the Ionian Islands.

The minister insisted, however, on delaying the dismissal until the Ottoman government could first legitimise its action by carrying out a formal judicial inquiry into Gregory VI's alleged misbehaviour.