He became Daijo-daijin (Grand Minister of State) in 1189 and made his daughter Ninshi KUJO marry the emperor to become Chugu (Empress) in 1190; it seemed that he turned into a powerful presence in the Imperial Court, but he could not easily control the government until 1192, perhaps due to the influence of Goshirakawa-in, and he was inevitably left out in the Imperial Court despite building a cooperative relationship with Yoritomo.
文治5年（1189年）には太政大臣となり、建久元年（1190年）には、娘九条任子を入内させて中宮に冊立、朝廷の第一人者に昇ったかに見えたが、建久3年（1192年）までは後白河院の影響力のため、容易に政権運営が出来ず、頼朝と協力関係を築いたが、反面、朝廷での孤立は否めなかった。