Greely was en route to his daughter's wedding on the morning of April 18, 1906, when the infamous San Francisco earthquake occurred. Brigadier General Frederick Funston, Greely’s second in command, immediately mobilized Presidio troops. When General Greely returned to the city on April 23, he found that 4,000 of his troops were in the city and authorized by Mayor Eugene Schmitz to shoot looters. Alarmed at the progression towards martial law, Greely assumed command and made it clear that the Army was subordinate to civil authorities.
Greely was reluctant in having the army involved in relief activities. His hesitancy may have stemmed from his broad political scope, as it may not have been the Army's organizational skills that the civilian leaders sought, but rather someone else to take the blame if relief efforts went awry. Discussing the civilian relief authorities, Greely wrote that they "look to me for final decisions and full responsibility which I am regularly assuming thus obviating embarrassments which surround men in civil life and subject to political and personal criticism." Aware of political implications, Greely nevertheless retained his integrity. When a woman complained that she was "forced to eat at the same table with a Negro" in a relief kitchen, the former commander of 81st Colored Troops gave no consolation. "Doubtless they are hungry. The Negro who sat next to me as I took my luncheon yesterday ate enormously," he replied.