On 13 June 2016, Laporte renewed his contract until 2020, with his buyout clause rising to an initial €65 million.
On 24 March 2016, in a 2017 European Under-21 Championship qualifier against Scotland in Angers, Laporte was stretchered off with a fracture and dislocation to his right fibula and ankle, concluding his season prematurely. Previously, in October 2015, he stated that he would consider representing Spain if rejected by France for UEFA Euro 2016.
In August 2016, at the behest of new national manager Julen Lopetegui, Laporte began the process of making himself eligible for Spain. A month later, he was called up to the senior France squad for 2018 World Cup qualifiers against Bulgaria and the Netherlands in October, and stated he had decided not to apply for Spanish nationality with the continued aim of playing for France. He did not take part in either match.