On September 12, 1855, Emerson married Sarah Maria Young, in Oswego, New York. Sarah was descended from the Young and Elsworth families of Revolutionary war fame.
Detachments of the 47th Missouri were involved in the Battle of Pilot Knob in September 1864. In October, he was tasked by General Rosecrans to reopen the Iron Mountain Railroad from St. Louis, Missouri to Pilot Knob. In this mission he was again wounded in battle.
In December 1864 Emerson's regiment was ordered to assist General George Thomas, at Nashville, Tennessee. His regiment pursued General Hood as far as Alabama, capturing more than 1000 prisoners. Emerson was in command of the regiment through the end of the war.
After the war
Emerson resumed his law practice at Ironton, and was appointed to the Judgeship of the Fifteenth Judicial Circuit Court, which he eventually resigned. After leaving the bench, he was appointed by President Grover Cleveland to the United States Marshall for the Eastern District of Missouri. He served in this capacity for four years.
Emerson Electric Company
In 1890, Emerson met two Scottish orphans, Alexander and Charles Meston, who wanted to manufacture electrical and mechanical devices. He provided $50,000 start-up capital and lent his name to a new corporation creating the "Emerson Electric Manufacturing Company", and served as the company's first President from 1890 to 1892.
In 1892, Emerson retired, selling his interest in Emerson Electric to Herbert L. Parker, a former railroad executive.