The ship conducted her normal peacetime training exercises in the first half of 1899, thereafter joining III Division for the annual maneuvers from 1 August to 16 September. She was decommissioned in early 1900 for an extensive reconstruction, which was carried out at the in Danzig. Work began on 15 May and was completed by mid-1902; after completing sea trials, she was recommissioned on 1 July under the command of KK Carl Paschen. She participated in the annual fleet maneuvers the next month, and after their conclusion in mid-September, she was decommissioned in Danzig on 25 September. Beowulf was not scheduled to be reactivated for the 1903 training year, but after Hagen suffered a breakdown that required extensive repairs, Beowulf was recommissioned to take her place in II Squadron on 8 July with KK Hartwig von Dassel in command. The fleet exercises concluded on 15 September, and unlike in previous years, Beowulf remained in service in II Squadron, though KK Franz von Holleben replaced Dassel at that time. She took part in a cruise to the Netherlands and Norway with the rest of the squadron in 1904. After the fleet maneuvers that year, Beowulf was replaced in the squadron by the pre-dreadnought battleship on 23 September and she was allocated to the Reserve Squadron. She was briefly reactivated in 1909 for the annual maneuvers, serving in III Battle Squadron under the command of KzS Gottfried von Dalwigk zu Lichtenfels.
