While in school, he published a satire and pinned it on the door of Dimitsana Pasha (the Turkish local governor at the time) signing it "Grigorios Phos Kalamios" (Φῶς Καλάμιος τό νομα Γρηγόριος).

Papaflessas was sent to the northern part of the Ottoman Empire to inspire and spread hope among his countrymen for the nation's independence from the Turks.

At the end of 1820, he sailed to Aivali of Asia Minor and catechised all scholars of the Big School (as it was called there) while awaiting the arrival of war supplies from Smyrna.

At the Saint George monastery he called a meeting of Greek authorities[8] and high priests to discuss if the time was right to start the a revolution.

Concerns about the practicalities of war and the uncertainty of the promises of military support led the other participants to propose to secretly jail Flessas in the monastery of Agia Lavra in order to avoid problems for the nation.

Flessas' problem was with the upper class (landowners) in the villages and municipalities, including the top echelon of the clergy, who did not trust Papaflessas, and his mission was received with a great deal of scepticism and fear.

He felt safer to first approach farmers and peasants, and the poor class of people who were easily magnetized by his speeches looked upon him as the messiah of their freedom.

After the meeting he went to Kalavryta and met with Nikolaos Souliotis and Asimakis Skaltsas in order for them to write a letter in the first ten days of March 1821 to Oikonomos Eliopoulos.

From Kalyvia he went secretly to Gardikion (now Amfeia) near his hometown Poliani and learned that the small boat of Mexis Poriotis arrived in Almyros.

In order to unload the boat they had to have the authorization of the area's harbourmaster, the famous Mavromichalis, who was in the pay of the Turks' security force.

This was agreed to and the supplies were transported to the monastery of Velanidia, where Papaflessas served as a monk, summoning prominent kleftes, chieftains from the area.

In Mani a gathering of the captains of the rebels had decided to start the revolution on March 25, 1821, but received news on the 22nd that the fighting had already begun.

The Greek War of Independence officially started on March 25, 1821, and brought a great change to the church of the free kingdom.

Realizing the great danger the nation was facing with the Ibrahim's invasion, he demanded the government grant amnesty to Kolokotronis and other political prisoners.

This demand was refused and he appeared before the executive branch and parliament to tell them he would go to Messinia alone to organize a resistance against Ibrahim, determined to return victorious or die in the battlefield.

The universal indignation now expressed at his conducts convinced him that it would be dangerous for him to remain in Nauplia, where his licentious life and gross peculation pointed him out as the first object of popular vengeance, and the scapegoat for the sins of his colleagues.

Papaflessas gathered 3,000 poorly armed men and went to the province of Pylia, Messinia, searching for the best spot to face Ibrahim's army coming out of the city of Pylos.

In speaking of Papaflessas after his death, it is said that Ibrahim told his officers: "If Greece had ten heroes like him, it would not have been possible for me to undertake the military campaign against the Peloponnese".