Pena Nieto boarded his plane looking forward to the first French visit by a Mexican head of state for 18 years where he was to sign "unprecedented" deals, according Vice-Minister for Foreign Affairs Carlos Alberto de Icaza.
By the time he touched down, 58-year-old Guzman had escaped from a maximum-security prison after spending just 17 months in jail.
Guzman had been the world's most-wanted druglord before his arrest, one of several narco-traffickers in Mexico where a drug war has cost 80,000 lives since 2006.
His arrest was big news and so is his escape.
It was bad news for Pena Nieto, who is to attend France's Bastille Day parade on Tuesday and watch Mexican troops and gendarmes lead the procession.
Their presence has been criticised by NGOs, who have promised to protest, pointing out that a UN official last year declared that torture by Mexico's military and police is "generalised" and practised with impunity.
Paris-based press freedom campaign, Reporters Without Borders, called on Pena Nieto to act to end violence against journalists in his country, where it says 86 journalists and media workers have been killed since 2000.
The visit is a sign of a thaw in relations with France, which hit a low-point over a campaign to free French national Florence Cassez, the girlfriend of a kidnapper who was jailed for 60 years but released in 2013.
Pena Nieto is to visit an Airbus factory, where he is expected to announce the purchase of several Super Puma military helicopters, and attend the unveiling of plans for a Mexican cultural centre on the banks of the river Seine in Paris.