The area is a high priority for EU leaders and have claimed that states will be allowed to join the crumbling bloc if they continue with economic and democratic reforms.
He added: “We are not stepping away, but stepping in.”
The Brussels bigwig has been criticised after rowing back on his claim that no new countries would be allowed to join the EU during his mandate at the Commission, which ends in 2019.
At a Brussels summit on Thursday, diplomats said European leaders would try to make regular visit to the Balkans to encourage reform.
A senior EU official said: “For the countries in the Balkans, that matters.
“There’s a sense that their European path has slipped away. But their only path is towards the EU.”
The Balkan countries are at different stages with their respective reforms, with Serbia considered a key state whose development could pull up others.
However, Serbia still refuses to recognise the independence of Kosovo, which could become a major issue as accession talks progress.
Albania, Bosnia, Kosovo, Montenegro and Macedonia are all apparently keen to join the bloc, but the latter is suffering a major political crisis which could hamper any bid to join the EU.
Meanwhile, Theresa May has pledged to hold a special summit on the Western Balkans in 2018, echoing Angela Merkel’s claim about the importance of the region.