The core activity of BALTDEFCOL is the Joint Command and General Staff Course (JCGSC). It is in most aspects similar to other one-year Joint Command and General Staff courses. Since 2004, BALTDEFCOL has established the Higher Command Studies Course (HCSC), which is an officer education level four course. The Civil Servants Course (CSC) is also run to prepare civil servants for national security and defence policy work.
The first Commandant of the BALTDEFCOL, the Danish Brigadier General M. H. Clemmesen (Danish Army), retired from his position in December 2004. The post is now being rotated between the three Baltic states.
In May 2005, the first Commandant of BALTDEFCOL was awarded with the St Germain Gold Medal of the Danish Military Society, the citation also mentioning his initiative and work with the establishment and running of the college.