Following the War, Ammen was assigned to the Naval Machinery at Charlotte, North Carolina in July 1865 and remained there until September that year, when he was appointed commanding officer of the monitor USS Miantonomoh.
He served with that vessel within the North Atlantic Squadron until March 1866, when he was detached for special duty in Hartford, Connecticut.
While there, Ammen was promoted to the rank of Captain on July 25, 1866.

He was appointed commanding officer of a newly commissioned screw steamer USS Piscataqua at Portsmouth Navy Yard and served within the Asiatic Station until February 1869.
During his service there, Ammen's vessel served as Flagship to Commanding admiral, Stephen C. Rowan.

Following his return stateside and leave with family, Ammen was appointed Chief of the Bureau of Yards and Docks in May 1869.
He was responsible for building and maintaining navy yards, drydocks, and other facilities relating to ship construction, maintenance, and repair until August 1871.

He was subsequently appointed Chief of the Bureau of Navigation and promoted to Commodore on April 1, 1872.
While in this assignment, his principal responsibilities were to provide nautical charts and instruments and to oversee several activities involved navigation research, including the Naval Observatory.
In 1872 he was appointed member of a commission to examine and report on the feasibility of constructing a canal through Nicaragua.
The commission reported in favour of the Nicaraguan route, which he strongly advocated.
He was promoted to Rear Admiral on December 11, 1877.
Ammen served with the Bureau of Navigation until his retirement from the Navy on June 4, 1878.
Following the War, Ammen was assigned to the Naval Machinery at Charlotte, North Carolina in July 1865 and remained there until September that year, when he was appointed commanding officer of the monitor USS Miantonomoh. He served with that vessel within the North Atlantic Squadron until March 1866, when he was detached for special duty in Hartford, Connecticut. While there, Ammen was promoted to the rank of Captain on July 25, 1866.
He was appointed commanding officer of a newly commissioned screw steamer USS Piscataqua at Portsmouth Navy Yard and served within the Asiatic Station until February 1869. During his service there, Ammen's vessel served as Flagship to Commanding admiral, Stephen C. Rowan.
Following his return stateside and leave with family, Ammen was appointed Chief of the Bureau of Yards and Docks in May 1869. He was responsible for building and maintaining navy yards, drydocks, and other facilities relating to ship construction, maintenance, and repair until August 1871.
He was subsequently appointed Chief of the Bureau of Navigation and promoted to Commodore on April 1, 1872. While in this assignment, his principal responsibilities were to provide nautical charts and instruments and to oversee several activities involved navigation research, including the Naval Observatory. In 1872 he was appointed member of a commission to examine and report on the feasibility of constructing a canal through Nicaragua. The commission reported in favour of the Nicaraguan route, which he strongly advocated. He was promoted to Rear Admiral on December 11, 1877. Ammen served with the Bureau of Navigation until his retirement from the Navy on June 4, 1878.
Daniel Ammen