One of the most important but also darkest cases of conspiracy during the first years after the establishment of the Greek state, was the one attributed to the Philorthodoxos Etaireia (pro-Orthodoxy Committee). It was revealed after it was denounced by a conspirator, who handed to the authorities documents incriminating Nikitas Stamatelopoulos, known as Nikitaras, the veteran chieftain, and George Kapodistrias, the younger brother of the Governor Ioannis Kapodistrias. According to these denunciations, the most important members of the Napaioi (the pro-Russian political party) were involved in the conspiracy, along with many members of the Russian diplomatic delegation in Greece. It was also claimed that this plot included the arrest of Otto and his coercion to either join Orthodoxy or resign. According to these denunciations, this act against Otto was to be realized during the New Year doxology (1840).

It seems that Philorthodoxos Etaireia was founded in June 1839 and the most eminent personalities of the Napaioi participated in it. Its general aim was to organize liberation movements in Epirus, Thessaly and Macedonia, reinforce Orthodoxy (abolishing the regulation on the ecclesiastical issue, having the king and royal family embrace the Orthodox dogma and prohibiting heterodox religious missions in the Greek state) and appoint exclusively natives in political, administrative and military posts. The organization of the Etaireia clearly recalled the conspiratorial ways of the Philiki Etaireia. Its members were only accepted after an initiation, and there were three grades in the hierarchy of members. Information on the aims of the Etaireia (liberation, protection of Orthodoxy, conspiracy) was given to members depending on their position. Finally, it seems that until the end of 1839, when the existence of Philorthodoxi Etaireia was revealed, its members had not come up with any particular plan of action. The disclosure of the conspiracy led to the arrest of Nikitaras and G. Kapodistrias; however, the other members managed to destroy documents and all other evidence which could have been incriminating. In spite of the fact that eminent Napaioi were watched closely (Gennaios Kolokotronis, Ioannis Goura Mamouris, George Glarakis) no incriminating evidence was presented in court on either the conspiracy or even the foundation of a secret committee. Thus, the accused were acquitted.

The foundation of the society was of a type of oppositional institution (conspiracy) which frequently appeared in Greek political life, especially during the first half of the 19th century. However, the importance of this particular movement went beyond the political field. It suggested, in particular, the dynamics of a tendency against the modernization of Greek society by showing the need to defend traditional values, primarily traditional religious worship. So this, mostly appearing in rural areas, became particularly evident in both the conflict on the ecclesiastical issue, and the revolts which broke out during the first decades after the foundation of the Greek state, while at the same time it embraced the Megali Idea (Great Idea) and irredentism.