On the second day of the battle, USS Monitor engaged CSS Virginia, allowing tugs to free Minnesota on the morning of 10 March.

Minnesota, carrying William B. Reed, appointed U.S. Minister to the Empire of China, departed from Norfolk, Virginia, on 1 July 1857 for the continent of East Asia.

She arrived at Hampton Roads, Virginia, on 13 May and the next day captured the schooners Mary Willis, Delaware Farmer, and Emily Ann.

When Flag Officer Louis M. Goldsborough relieved Stringham in command of the North Atlantic Blockading Squadron on 23 September, he selected Minnesota as his flagship.

While blockading off Hampton Roads, 8 March 1862, Minnesota sighted three Confederate warships, Jamestown, Patrick Henry, and led by the unique revolutionary appearance of the CSS Virginia—the former USS Merrimack, (the 1855 steam-powered heavy frigate, rebuilt since burnt/scuttled in 1861 and now protected by riveted iron plates) — rounding Sewell's Point from Norfolk and the Elizabeth River, and heading north across the Hampton Roads harbor to the northern peninsula toward Newport News, Virginia.

"All on board felt we had a friend that would stand by us in our hour of trial," wrote Captain Gershom Jacques Van Brunt (1798-1863), the stranded and damaged Minnesota vessel's commander, in his official report to the Navy Department, the day after the engagement in Hampton Roads.

[3] Virginia fired from her rifled bow gun a shell which passed through the wooden Union warship's chief engineer's stateroom, through the engineers' mess room, amidships, and burst in the boatswain's room, exploding two charges of powder there, starting a fire onboard the vulnerable wooden frigate which was promptly extinguished.

At midday Virginia withdrew southwards back toward Norfolk, and the Union Navy tugs resumed its efforts to refloat Minnesota.

Early the next morning, the 1859 side-paddlewheel steamship S. R. Spaulding (on duty as a hospital ship with the Hospital Transport Service of the United States Sanitary Commission) joined the several tugs and managed to pull free and refloat the heavy frigate, and she sailed east and anchored under the protecting guns opposite Fortress Monroe (still Union-occupied) at Old Point Comfort for temporary repairs.

However, Union General Benjamin F. Butler (1818-1893), withdrew his troops, nullifying the previous gains won by the joint Army-Navy effort.

This operation finally after four years of effort closed outside access to the city and port of Wilmington, denying the collapsing southern Confederacy the use of this very last open invaluable major seaport, just three months before the end of the war in the East.

Recommissioned again after eight years on 12 June 1875, she remained at the New York Navy Yard as a gunnery and training ship for naval seamen apprentices.

[11] In October 1895, Minnesota was loaned to the Massachusetts Naval Militia, continuing that duty for six years until August 1901 when she was sold by the government to the Thomas Butler & Company of Boston.