SECI has made a deliberate effort to inform and coordinate all its activities with the European Commission (EC) and related EU policies. EC experts participated in SECI ground-setting activities and project groups meetings and contributed with expertise and advice. SECI held ad hoc coordination meetings in Brussels with EC officials and experts where joint strategies in the region were discussed.

EU coordination activities continue on policy level through the SECI Coordinator, who is in constant contact with all relevant parts of the Commission. This coordination aims at establishing proper channels of communication, clarify EC's role in SECI activities and, most importantly, lay the foundations for a consultative process on both policy and technical levels. Apart from this direct communication the relevant EC directorates and offices are regularly informed on the activities undertaken by the Initiative. This close cooperation is crucial to streamlining activities within specific areas, especially since SECI States find themselves at a different stage of the EU integration process from legal point of view