After Yoritomo died, Nagakiyo was implicated in the Rebellion of Yoshikazu HIKI and accordingly he was punished because his son had been an attendant of the second Shogun MINAMOTO no Yoriie, and owing to this incident, the Ogasawara clan fell at one time, but he became the 'deputy of the seven provinces' as one of the Daishogun (commander in chief) of Tosando and made a great contribution to the Jokyu War, and thanks to this achievement he became the Awa no kuni shugo (provincial constable of Awa Province) in 1221.
頼朝の没後、子の弥太郎長経が二代将軍源頼家の近習であった事から、比企能員の変に連座して処罰されたため一時小笠原氏は没落するが、承久の乱で東山道の大将軍の一人として「七ケ国管領」となり功績を挙げ、承久3年（1221年）に阿波国守護となる。