With guerrillas harassing his line of communications back to Veracruz, Scott decided not to weaken his army to defend Puebla but, leaving only a garrison at Puebla to protect the sick and injured recovering there, advanced on Mexico City on August 7 with his remaining force. The capital was laid open in a series of battles around the right flank of the city defenses, the Battle of Contreras and Battle of Churubusco. After Churubusco, fighting halted for an armistice and peace negotiations, which broke down on September 6, 1847. With the subsequent battles of Molino del Rey and of Chapultepec, and the storming of the city gates, the capital was occupied. Scott became military governor of occupied Mexico City. His victories in this campaign made him an American national hero.

The Battle of Chapultepec in September 1847 was a siege on the castle of Chapultepec, built on a hill in Mexico City in the colonial era. At this time, this castle was a renowned military school in the capital. After the battle, which ended in a victory for the U.S., the legend of "Los Niños Héroes" was born. Although not confirmed by historians, six military cadets between the ages of 13 and 17 stayed in the school instead of evacuating. They decided to stay and fight for Mexico. These Niños Héroes (boy heroes) became icons in Mexico's patriotic pantheon. Rather than surrender to the U.S. Army, some military cadets leaped from the castle walls. A cadet named Juan Escutia wrapped himself in the Mexican flag and jumped to his death.