 For this disappointing position, Stramaccioni was sacked and replaced by Walter Mazzarri, where Jonathan secured a more regular place at starting lineup.On 18 August 2013, in the opening match of the 2013–14 season, against Cittadella in third round of Coppa Italia, Jonathan scored his first goal of the season after he beat goalkeeper Raffaele Di Gennaro with a header, following a cross from Fredy Guarín.Inter won the match 4–0.