When hostilities with the Barbary States closed in 1805, Heermann returned to the Unitied States, but soon took leave of absence to study in Europe until 1808 when he returned to active duty in Norfolk, Virginia. Largely due to his pleas for better medical care for the men of the Navy, Congress passed a bill authorizing the construction of hospitals at several naval stations, but the first official U.S. Naval Hospitals were not actually built until after Dr. Heermann’s death.
He was transferred to New Orleans in August 1811; and, with the exception of a year in the North for his health and an assignment 11 June 1830 in the Mediterranean, where he served for an unknown time as Fleet Surgeon of the US Squadron, he remained there until he died in May 1833.