 On 18 August 2013, in the opening match of the 201314 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. Musi wa18 Nyamavhuvhu 2013, mumutambo wekuvhura mwaka wa2013-14, vachipesana neCittadella mumutambo wechitatu weCoppa Italia, Jonathan akarova chibodzwa chake chekutanga chemwaka mushure mekurova muchengeti wepagedhi Raffaele Di Gennaro nemusoro, zvichitevera muchinjikwa kubva kuna Fredy Guarín. Inter yakakunda mutambo wacho 40. Mumutambo wokutanga wemwaka mutsvaMuSerie A, Jonathan akabatsira chinangwa chekutanga chaYuto Nagatomo mukukunda 2-0 pamusoro peGenoa, achibatsira timu kuti itange zvakanaka. Mumutambo wechipiri musi wa1 Gunyana, Jonathan akaita rubatsiro rwake rwechipiri mwaka uyu nekupa Rodrigo Palacio chinangwa chekutanga chekukunda 3-0 kure neCatania. Musi wa 26 Gunyana, Jonathan akarova chibodzwa chake chekutanga cheligi neInter mukukunda 2-1 kuSan Siro vachipesana neFiorentina, zvichipa timu yake mukana muminiti yechi83 mushure mekupfura kwakasimba kubva mukati mebhokisi. Mwedzi mumwe gare gare, Jonathan akarova muchengeti mukukunda 4x2 pamusoro peHellas Verona ichangobva kukwidziridzwa, iyo yakarambidzwa sechinangwa. Jonathan akarova kechipiri muSerie A, achienzanisa mu1 1 kure kure neBologna musi wa24 Mbudzi. Jonathan akaenderera mberi nehunhu hwake hwakanaka, achipa rubatsiro rwake rwechitatu mumwaka uyu mukukwikwidza 3-3 vachipesana neParma kuSan Siro, achibatsira Rodrigo Palacio muminiti yechi44 yemutambo. 