Kammala wannan jumlar: Yin kawancen siyasa tare da Empress Dowager, kuma ya zama abokin gaba na dindindin na Sarkin Guangxu, Yuan ya bar babban birnin a 1899 don sabon nadin sa a matsayin Gwamnan Shandong. A lokacin mulkinsa na shekaru uku ne Rikicin Boxer (1899<unk>1901) ya barke; Yuan ya tabbatar da murkushe 'yan dambe a lardin, kodayake dakarunsa ba su taka rawa a waje da Shandong kanta ba. Yuan ya ɗauki bangaren ƙungiyar masu goyon bayan baƙi a cikin Kotun Masarauta, tare da Yarima Qing, Li Hongzhang, da Ronglu. Ya ƙi tsayawa tare da 'yan dambe kuma ya kai hari ga sojojin Alliance na Kasashe Takwas, tare da shiga tare da sauran gwamnonin kasar Sin waɗanda suka ba da umarnin manyan sojoji na zamani kamar Zhang Zhidong ba sa shiga cikin Tawayen Boxer. Shi da Zhang sun yi biris da sanarwar yaƙi da Empress Dowager Cixi ta yi wa ƙasashen waje kuma sun ci gaba da danne 'yan dambe. An san wannan rukunin da ake kira The Mutual Protection of Southeast China. Baya ga rashin yin yaƙi da Allianceungiyar Al'umma Takwas da kuma danne 'yan dambe a Shandong, Yuan da rundunarsa (Right Division) sun kuma taimaka wa Allianceungiyar Al'umma Takwas don danne' yan dambe bayan
Ƙungiyar ta kama Beijing a watan Agustan 1900. Sojojin Yuan Shikai sun kashe dubun dubatar mutane a yakin da suka yi da 'yan dambe a Zhili. Yuan ya yi aiki daga Baoding a lokacin yakin, wanda ya ƙare a 1902.