Phelps served aboard the "Bonita" and "Jamestown" during the Mexican–American War, giving naval support to Winfield Scott's Army during the Siege of Veracruz. Much of his time was also spent patrolling the Mexican coast on blockade duty. In little time Phelps had already developed strong opinions about how the war should be conducted, and was displeased that the Navy was lending much of their service protecting merchant ships while sailors were coming down with scurvy for want of provisions.