Rubuta ci gaba don wannan sakin layi - A ranar 13 ga Yuli, 2011, an sanar da cewa Jonathan zai bar Santos don horar da ƙattai na Serie A Inter Milan, har sai an kammala canja wurin. Kwana biyu bayan haka, a ranar 15 ga Yuli, ya zama dan wasan Inter a hukumance, ya sanya hannu kan kwangilar shekara huɗu. Jonathan ya fara bugawa Inter wasa a ranar 11 ga Satumba 2011 a mako na biyu na 2011-12 Serie A
, yana wasa cikakkun mintuna 90 a cikin rashin nasara 4-3 zuwa Palermo. Kwana uku bayan haka Jonathan ya fara buga gasar zakarun Turai, inda ya buga wasan gaba daya a ranar wasa ta 1 da kungiyar Trabzonspor ta Turkiyya a wasan da suka yi rashin nasara a San Siro.