It appears that he intended to take up the position of his father vis-a-vis the papacy and to return to unfriendly relations with the duke of Apulia, for Gregory visited Capua a mere three months after Richard's death and Jordan, probably with papal prodding, began fomenting revolt in the Guiscard's lands.
In 1085, on Robert's death, Jordan supported Bohemond, the elder son, over Roger Borsa, the eldest by Sikelgaita, who was his own sister-in-law, he having married Gaitelgrima, another daughter of Prince Guaimar IV of Salerno.
In hopes of curbing the influence of Clement and united his interests with those of the papacy once again, he pressured the College of Cardinals to elect Desiderius of Montecassino as successor Gregory.
The pope remained lukewarm to his new job until Jordan suggested that only through decisive action could the good fortune of his beloved abbey of Montecassino be sustained.
The remainder of Jordan's career was not notable and he died in November 1090 or 1091 in Piperna (near Terracina) and was buried in the monastery he had long supported, Montecassino, leaving a young son named Richard who succeeded him.