The London Declaration of Jul. 1990 was a decisive turning point in the history of the Alliance and led to the adoption of the new Alliance Strategic Concept in Nov. 1991, reflecting a broader approach to security. This in turn led to NATO's Long Term Study to examine the Integrated Military Structure and put forward proposals for change to the Alliance's Force Structures, Command Structures and Common Infrastructure.

In essence, the Cold War command structure was reduced from 78 headquarters to 20 with two overarching Strategic Commanders (SC), one for the Atlantic, and one for Europe, with three Regional Commanders under the Supreme Allied Commander, Atlantic (SACLANT) and two under the Supreme Allied Commander, Europe (SACEUR). During the 2002 Prague Summit, NATO's military command structure was again reorganized with a focus on becoming leaner and more efficient. The former Allied Command Europe (ACE) became the Allied Command Operations (ACO).

The Supreme Allied Commander Europe and his staff at Supreme Headquarters Allied Powers Europe (SHAPE) situated in Mons, Belgium, were henceforth responsible for all Alliance operations, including those previously undertaken by SACLANT. The latter has now become Allied Command Transformation (ACT) headquartered in Norfolk, Virginia. Commanded by Supreme Allied Commander Transformation (SACT), it is responsible for promoting and overseeing the continuing transformation of Alliance forces and capabilities, especially through training and development of concepts and doctrine.

The command structure beneath SHAPE was also significantly streamlined, with a reduction in the number of headquarters from a total of 32 to nine.