During an air attack on the night of 26 - 27 February 1942, while under repair at the dry-dock at Deutsche Werke in Kiel. The Gneisenau received a direct hit on the foredeck. Despite orders her stocks of ammunition were not removed. This was a fatal error, as the hit she received started a chain reaction which devastated the ship and killed 112 crewmembers.

This was the end of the career of the Gneisenau.

She was move to Gdynia in 1942 to await repairs. Although some work was done from 1942 through to 1944 to reconstruct her, she was withdrawn from service in July 1943 to allow the replacement of the 28cm battery with twin 38 cm (15 in) turrets. After the sinking of the Scharnhorst, this work was finally abandoned.

In this enlargement you can see her damaged stem has been cut off and later was used as scrap metal. Also you can see that her main gun turrets have been removed.

Her aft main turret, "Caesar" was converted to a coastal battery named Austråt Fort in Ørland near Trondheim, Norway and still exists today.
In Denmark, at the former "Stevnsfort" near Rødvig, two twin 15 cm turrets from her secondary armament still exist.