In his final years, discord arose between him and Michiie regarding government policies and over plans for court appointments, and then Kanetsune KONOE, who became Sekkan (Regent) after Michiie, married Michiie's daughter, but thereafter Kintsune saw to it that Yoshizane KUJO (whom Kintsune had raised), who got along even worse with Michiie despite being Michiie's second son, was installed as Sekkan, insuring he could continue to manipulate court appointments as he saw fit.
晩年は政務や人事の方針を巡って道家と不仲になったが、道家の後に摂関となった近衛兼経と道家の娘を縁組し、さらに道家と不和であった道家次男の九条良実（公経が養育していた）をその後の摂関に据えるなど朝廷人事を思いのままに操った。