The staff of these former branch commands continued to exist inside FKO, but in 1982, which saw a major reconstruction of FKO, they too vanished in favour of an even more branch independent organisation.

Between 1973 and 2006 FKO was located in Vedbæk (Henriksholm Allé) a little north of Lyngby, in a modern steel and concrete building, built 1970 – November 1972 by Defence Construction Service.

FKO moved to Søarsenalet on Holmen Naval Base on July 24, 2006.

As a result of the Danish Defence Agreement 2013–17, the FKO saw major structural reorganization, to such an extent that it was renamed Joint Defence Command (Danish: Værnsfælles Forsvarskommando).

[3] On 1 January 2019, as part of the Danish Defence Agreement 2018–23, the name was reverted to the previous name.