Up to 1,000 French and Turkish left-wingers, Armenians, Kurds and members of the Alevi religious community protested against Erdogan’s visit, accusing him of human rights abuses and repression of last year’s Gezi Park demonstrations.
Erdogan was touring European ahead of August elections, in which Turkish citizens abroad will be able to vote for the country's president for the first time.
Erdogan hasn't yet declared himself a candidate but is widely expected to stand for the post after more than 11 years as premier.
In Lyon he met members of the city’s Turkish community, urging them not to forget their "culture, traditions, identity and especially faith" while integrating in France.
On Friday he met President François Hollande at the Elysée presidential palace.
He has already been to visit Turks in Germany and Austria and was greeted by 100,000 opponents in Vienna.
These foreign constituencies are important to Erdogan, as his image has suffered less damage among expatriate Turks than it has at home, Dorothée Schmid of the French Institute for International Relations told RFI.