[63] The incident made it look like he had fainted, causing one soldier to call for someone else to take command, "General Pierce is a damned coward."[64] Pierce returned for the following day's action, but re-injured his knee, forcing him to hobble after his men; by the time he caught up, the battle was mostly won.[64]
As the Battle of Churubusco approached, Scott ordered Pierce to the rear to convalesce. He responded, "For God's sake, General, this is the last great battle, and I must lead my brigade."Scott yielded, and Pierce entered the fight tied to his saddle, but the pain in his leg became so great that he passed out on the field. The Americans won the battle and Pierce helped negotiate an armistice. He then returned to command and led his brigade throughout the rest of the campaign, eventually taking part in the capture of Mexico City in mid-September, although his brigade was held in reserve for much of the battle.[65] For much of the Mexico City battle, he was in the sick tent, plagued with acute diarrhea.