"The coming months will show us how far we can go together with Turkey, " Von der Leyen concluded.
Turkish President Recep Tayyip Erdogan has confirmed during talks with the heads of the European Commission and European Council on Tuesday that Turkey remained committed to entering the bloc, his spokesman, Ibrahim Kalin, said.
Issues also included Turkey's gas exploration project in the eastern Mediterranean and future talks about the divided island of Cyprus. Erdogan's efforts at reconciliation followed a flare up of tensions previous year over Turkey's decision to stop deterring migrants from crossing its border into Greece, as well as over the dispatching of Turkish research ships into waters claimed by Greece and Cyprus.
Michel acknowledged a de-escalation in the region, but said it must be "sustained and enhanced". "Our engagement will be progressive, proportional and reversible. And we hope Turkey will seize this window of opportunity". "We urge Turkey to reverse its decision because it is the first worldwide binding instrument to combat violence against women and children", she said.
"For its part, the European Union is ready to walk the talk". Charles Michel has also been criticised for taking his seat and not standing up for Mrs von der Leyen.
The meeting comes on the heels of Turkey's withdrawal last month from a treaty combating violence against women and the launch of a formal bid to shut down the country's main pro-Kurdish party.
The EU chiefs, who last held in-person talks with Erdogan a year ago, were expected to present Ankara with three options if the maritime de-escalation continues, including improving economic ties, a formula to support the more than 4 million refugees in Turkey, and ways to increase contacts.
Turkey cares for nearly 10 million Syrian refugees both within Turkey and Syria, and Turkish officials have suggested they would need more financing to help.
Last month, Erdogan pulled Turkey out of a key European convention aimed at combatting violence against women, triggering criticism from EU officials. This would bring European Union candidate Turkey into the internal market of the world's largest trading bloc and allow unhindered flow of goods and services.
Meanwhile, in an interview on Monday with Greek television ERT, President Nicos Anastasiades underlined his determination to take part in the informal conference on Cyprus in Geneva.
"We have achieved a number of convergences, the legislative and judicial authority issues have been agreed", the President remarked, noting that significant issues are still pending - the executive issue at some point, property, territorial adjustments and the issues of guarantees and the presence of troops on the island.
The Turkish government did not immediately respond to a request for comment on the matter.
Nonetheless, he would be going to the conference with a "positive attitude".
President Anastasiades urged Ankara to realise that its aim for two states is considered unacceptable by all, including the US, Russia, China and other permanent and non-permanent members of the United Nations and the EU.
"The president of the commission was clearly surprised", European Commission spokesman Eric Mamer said, insisting von der Leyen should have been treated "exactly in the same manner" as Michel.
A Turkish diplomatic source told AFP that Ankara expects the modernisation of the 1995 Customs Union and greater emphasis on Turkey's candidacy status to join the EU. She will have separate meetings with Anastasiades, Turkish Cypriot leader Ersin Tatar and Foreign Minister Nikos Christodoulides.