quality:corruption
Opposition to Uthman

Upon his return to Medina, Amr divorced Umm Kulthum and openly criticized Uthman. The Caliph and Amr engaged in a number of heated public exchanges and, according to a report in the Islamic traditional sources, Amr incited Muhammad's senior companions Ali, al-Zubayr and Talha ibn Ubayd Allah, as well as the Hajj pilgrims in Mecca, against Uthman. He lobbied Muhammad's wife A'isha for support and the latter pressed Uthman to reappoint Amr to Egypt citing its garrisons' satisfaction with his rule. In a sermon at the mosque in Medina in June 656 and a letter penned to the Muslim leaders in Syria, Uthman mentioned that he had intended to reappoint Amr but did not follow through as a result of the latter's excessive insult. According to the historian Wilferd Madelung, the insult Uthman cited was likely Amr's public reaction to the Caliph's statement that the mutinous Egyptian troops who had arrived in Medina to protest the Caliph's policies had withdrawn because they were misinformed: "Fear God, Uthman, for you have ridden over abysses and we have ridden over them with you. So repent to God, that we may repent".

After his last exchange with Uthman, Amr retired to his estate in southern Palestine. The estate was called "Ajlan" after one of his mawālī (non-Arab, Muslim freedmen) and was located in the vicinity of "al-Sab'", which had conventionally been identified with modern Beersheba, but more likely corresponds with Bayt Jibrin, according to the historian Michael Lecker; the medieval historians al-Baladhuri (d. 892) and Yaqut al-Hamawi (d. 1226) also suggest that Ajlan was located in the area of Bayt Jibrin. Amr had likely become owner of the estate through a caliphal grant, though he possibly could have taken possession of it in the course of his conquest of Palestine and his ownership had been confirmed by the caliphs. He lived on the estate, where he derived agricultural revenue, with his sons Muhammad and Abd Allah.

At his estate Amr received news of the siege of Uthman's house and the Caliph's subsequent assassination by Amr's Egyptian partisans. The roughly 400–600 Egyptian mutineers had protested Uthman's fiscal centralization policies in Medina and accused him of favoring his relatives over the early Muslim converts. The Caliph persuaded them to withdraw, but after they intercepted a letter on their departure ordering Ibn Abi Sarh to punish them, they turned back and assaulted Uthman in his home. In an anecdote cited by al-Baladhuri, Amr is quoted taking partial credit for Uthman's killing. Ali succeeded Uthman, but did not reappoint Amr to his post in Egypt. Amr was one of a number of figures held culpable for Uthman's death by the slain caliph's clan, the Banu Umayya (Umayyads), most prominently by Uthman's uterine brother and Amr's former brother-in-law al-Walid ibn Uqba. Nonetheless, the governor of Syria —which included Palestine—the Umayyad Mu'awiya ibn Abi Sufyan, had left Amr on his estate undisturbed. As pressure from the Umayyads increased against him, Amr distanced himself from any role in Uthman's death and wrote Mu'awiya to execute or banish the participating Egyptian troops who had been apprehended when they passed through Mu'awiya's jurisdiction on their way back to Egypt.