SECI actively encourages the involvement of other regional initiatives such as the Central European Initiative (CEI), the Adriatic-Ionian Initiative (AII), the Royaumont Process and the Black Sea Economic Cooperation (BSEC), and emerging regionally owned cooperation processes such as the South East European Cooperation Process (SEECP) and the Danube Cooperation Process (DCP). SECI has made a conscious effort to involve these initiatives into its project groups and activities at all times and keep consultative and informative communication concerning relevant ongoing matters and activities. 

Institutions with regional focus are also encouraged to contribute and participate actively. SECI has worked closely with the Institute for the Danube Region and Central Europe (IDM Vienna), the Centro Studi Nord Est (Venice and Trieste), WCO's Regional Intelligence Liaison Office (RILO-Warsaw), and the United Nations Center for International Crime Prevention, just to name a few. 

SECI has also concluded a Memorandum of Understanding on institutional cooperation with the EastWest Institute (EWI), a prestigious transatlantic think and action tank. On the basis of this MoU, the EastWest Institute was able to help coordinate activities of the SECI BAC and SECI PRO, as well as promote and incorporate the results of SECI's work in seminars and workshops organized by EWI. The EastWest Institute is observing developments in the region through the Action Network for South Eastern Europe (ANSEE).

A selection of Memorandums of Understanding, concluded with relevant regional organisations and initiatives within the framework of SECI, can be found in the SECI Library section.