At the start of the civil conflicts, in 1823, Ioannis Makrygiannis initially found himself on the side of the Kolokotronis faction. However, coming into conflict with Gennaios Kolokotronis, he placed himself under the orders of his opponents and fought against Kolokotronis' portion in Tripolitsa, which the government officials occupied in March 1824.
Makrygiannis was named lieutenant general by the government officials. In the meantime, however, the war situation began to press. While the victorious government officials of Kountouriotis were celebrating their victories, the bad news arrived. The Turks had destroyed Psara. Even worse events will soon follow. Makrygiannis, however, was sent by the government to Hydra, to protect the island from a possible Turkish landing. However, he was soon recalled to Argos and, together with Papaflessa, undertook a new campaign against the Kolokotronians.
The governors defeated and plundered areas of Arcadia and Messinia. Makrygiannis claims, in his memoirs, that he was unable to impose his authority on his disorderly men, who carried out the looting. At Kalyvia in Tripolitsa, Makrygianni's men killed Panos Kolokotronis, the son of the Elder of Moria.
Throughout the civil conflict, Makrygiannis reports that the Kountouriotis government lavishly paid the Roumeliotian troops to fight the Peloponnesians. This money came from the infamous English loan and instead of being used for the freedom of the homeland , were spent on dealing with political opponents of the regime.
In November 1824 Makrygiannis was sent to Athens, as a government emissary, to persuade Goura and other chieftains to come to the Peloponnese to fight. Makrygiannis was appointed garrison commander of Nafplion and in this capacity took part in the battles against the military in the area of Corinth. The government officials prevailed and Gouras proceeded to incredible looting. At the same time, other government forces, under Karaiskakis, plundered the region of Aegion. Makrygiannis then began to understand the damage caused by the civil conflict and exclaimed:"God, give us knowledge and virtue to save ourselves, not to perish prematurely!".
He himself, as he writes, forbade their men - about 350 - to loot. But when they saw what Gouras did to his people, they stopped obeying Makrygiannis and followed the same tactics. Of every village they left, only the walls of the houses remained ! Makrygiannis was forced to severely punish four of his soldiers who were stealing and looting. However, this punishment was a drop in the ocean.
The devastation and hatred ignited by the civil strife almost had a disastrous effect on the outcome of the revolution. Unfortunately, we Greeks do not learn from our mistakes. Completely disgusted by the situation, Makrygiannis returned to Nafplion. There Makrygiannis presented himself to the administration and denied any further involvement in the civil conflicts.
"I told the Government that I am in a civil war, and breaking laws, I am not fooled, I asked them to give me an order to go to Roumeli to fight for the Turks, either to disband my body or send another and I sit as a simple citizen, but I don't listen to an order for a civil war," he says.
Nevertheless he was ordered to go to Arcadia. In the meantime Ibrahim landed in the Peloponnese. The Greek forces, under Kountouriotis himself, were soundly defeated by Ibrahim, in the battle at Kremmidi. Then the Egyptian warlord besieged the fortresses of Navarino. Makrygiannis was, during this period, in Arcadia. When he learned what was happening he tried to go and fight with his men. However, the heads of government in the area did not let him go because they feared for their safety. But his men didn't show much enthusiasm either. "Half of them were in favor of me, let's go, half of them turned around, and the Government, they told me, didn't appoint us for the Arabs, they appointed us for Arcadia".
Finally, Makrygiannis, with some of his men, went to Navarino and fought Ibrahim, holding the castle of Neokastro, for several days, until he surrendered it by treaty and went to Kalamata in a British ship, with those men who had survived him. Near Kalamata he met Papaflessa for the last time who was on his way to meet his fate in Maniaki. He told Makrigiannis to follow him. But the latter refused, as his men were unarmed and many of them wounded.
Makrygiannis with his men arrived at Tripolitsa. But there he had to face a rebellion of his men, who demanded wages and compensation for the valuable weapons they had been forced to leave in Neokastro . Makrygiannis paid them at his own expense. After this he went to Nafplio, but the government ordered him to return to Tripolitsa, in order to hold the city against the approaching phalanxes of Ibrahim. But on his way to Tripolitsa he learned that the city had already been conquered.