"Imperator Nikolai I" returned to the Mediterranean in September 1901 and remained there until the Russo-Japanese War when she was transferred to the Baltic to be refitted in late 1904 to serve as the flagship of the Third Pacific Squadron under Rear Admiral Nikolai Nebogatov. The squadron departed Liepāja on 15 January 1905 for the Pacific. She was slightly damaged during the Battle of Tsushima, receiving one hit from a twelve-inch gun, two from eight-inch guns and two from six-inch guns, and suffered only 5 killed and 35 men wounded. She was surrendered, along with most of the Third Pacific Squadron, by Admiral Nebogatov the following day.