At a very early stage in the fighting, the question of the governance of the liberated territories came to light. Initially no fewer than three provisional governments coexisted, while in 1822 a constitution, which by the standards of the day was highly democratic, was adopted with the hope of securing the support of the people in Europe. A revised constitution was adopted in 1823, at which time the three local governments were unified in a central authority. However, unification did not bring unity. Feuding between rival groups culminated in outright civil war in 1824, prompting one chieftain, Makriyannis, to protest that he had not taken up arms against the Turks in order to end up fighting Greeks.

Such factionalism derived from a number of causes. There was a basic tension between the kodjabashis, or notables, of the Peloponnese, who were anxious to ensure that they retained the privileged status they had held under the Ottomans, and the military element, associated with such klephtic leaders as Theodoros Kolokotronis, who sought recognition in terms of political power for their contribution to the war effort. The island shipowners, whose contribution to the prosecution of the war at sea was vital, likewise laid claim to a share of power, while the small intelligentsia argued for the adoption of liberal parliamentary institutions. To some degree the clash can be seen as a confrontation between Westernizers and traditional elites and to some degree as a clash between the military and civilian parties. The Westernizers, who were nationalistic and whose attitudes were expressed by their adoption of a Western lifestyle, wanted independent Greece to develop along the lines of a European state, with a regular army and with a curb on the traditional powers of the church. The traditional elites, on the other hand, tended to see the struggle in terms of a religious crusade against the Muslims, and their national consciousness was less fully articulated. Anxious to maintain the power and privileges they had enjoyed before the struggle began, they were chiefly concerned with substituting the oligarchy of the Turks with one of their own.

The insurgents could not permit internecine fighting. Mahmud II had by this time forged an alliance with his nominal subject, Muḥammad ʿAlī, the ruler of Egypt, and his son Ibrahim Pasha, who were promised lavish territorial rewards in return for their assistance in suppressing the revolt. Beginning in early 1825, Ibrahim Pasha engaged in a bitter war with the insurgents. As their initially favourable military position deteriorated, the insurgents looked increasingly for salvation from the great powers (Russia, France, and Great Britain), which, from a combination of mutual suspicion as to each other’s objectives and concern at the damage being done to their commercial interests, gradually moved toward a more interventionist position.

In 1826, by the Protocol of St. Petersburg, Britain and Russia committed themselves to a policy of mediation, to which France became a party through the Treaty of London of 1827. A policy of “peaceful interference,” as the British prime minister Lord Canning described it, culminated in the somewhat planned destruction of the Turco-Egyptian fleet by a combined British, French, and Russian fleet at the Battle of Navarino in October 1827, the last great naval battle of the age of sail. This intervention by the great powers was instrumental in ensuring that some form of independent Greece came into existence, although its precise borders, which ran from Árta in the west to Vólos in the east, took some years to negotiate. This process was overseen by Count Ioánnis Kapodístrias, who was elected the first president of Greece by the Assembly of Troezene, which in 1827 enacted the third constitution of the independence period. Besides overseeing the negotiation of the boundaries of the new state, in which his extensive diplomatic experience in the Russian imperial service was fully employed, Kapodístrias was also completely engaged in trying to establish the infrastructure of a state in a country that had been ravaged by a vicious and destructive war. Schooled in the traditions of Russian autocracy, Kapodístrias chafed under the provisions of the 1827 constitution, which, like its predecessors, was a remarkably liberal document, and he abolished it. His paternalist and authoritarian style of government offended a number of key elements in the hierarchy of the embryonic Greek state. Growing unrest culminated in his assassination in Nauplia (Návplio), the provisional capital, in October 1831.