Soon after the battle, he married the daughter of a prominent Athenian, and his activities were thereafter inextricably linked with that city until his death. After Athens was captured by Ibrahim Pasha in June 1826, Makriyannis helped organise the defence of the Acropolis, and became the provisional commander of the garrison after the death of the commander, Yannis Gouras. He managed to repel a fierce assault against the Odeon of Herodes Atticus on 7 October, and during the defence of the Acropolis, he sustained heavy injures three times, to the head and to the neck. These wounds troubled him for the remainder of his life, but they did not dissuade him from taking part in the last phase of the war: in the spring of 1827 he took part in the battles of Piraeus and the battle of Phaleron.