Ihsanoglu was in Brussels for the opening of a permanent OIC observer mission in Brussels. Barroso said both sides discussed the security challenges in the Middle East and North Africa in the wake of the democratic movements dubbed the Arab Spring.
"Both leaders concurred that political polarization and huge economic and social needs have to be addressed to prevent instability from growing," a statement from Barroso's office said.
In a separate statement, Ihsanoglu said he welcomed a peace agreement between the Malian government and Tuareg rebels brokered last week with the help of the Economic Community of West African States.
The French and other European governments pledged billions of dollars in support to Malian recovery during a June donors conference. Mali called in support from former colonial power France to help fight insurgents who seized territory following a 2012 coup.
Barroso said the respect for democracy, the rule of law and freedom of religion were integral to ensure the success of democratic transitions under way in the region.