Juncker's comments came a day after Turkish President Recept Tayyip Erdogan gave a hardline speech to parliament on the anniversary of the attempted coup, following mass rallies in Ankara and Istanbul.
"Whoever wants to join the European Union is joining a union of values," Juncker wrote in an op-ed for German weekly Bild Sonntag, AFP reported.
"Europe's hand remains outstretched," he added, but it expects that "Turkey too should clearly show its European colors and emphatically take basic European values to heart."
In his speech, Erdogan vowed to sign any bill lawmakers pass on reintroducing the death penalty -- seen as a red line that would shut down Turkey's hopes of joining the EU.
"We will chop off the heads of those traitors" he told a crowd of hundreds of thousands in Istanbul.
The European Commission is in charge of accession negotiations for prospective new members, with Turkey's dossier largely frozen since last July's violence.
In his article, Juncker warned in particular against the detention without trial of journalists including Deniz Yucel of German daily Die Welt.
This was "in no way compatible with a union of human rights, press freedom and the rule of law," he said.
Following last year's coup bid, Erdogan embarked on the biggest purge in Turkey's history, arresting 50,000 people and sacking almost three times as many.
He also shored up his position by winning a referendum on enhancing his powers earlier this year.