Tuhia he tohutoro mō tēnei wāhanga - I te tīmatanga o te Pakanga ā-Iwi i te tau 1861, ka wehe atu a Magruder i te ope taua o te Kotahitanga ki te whakaae ki tētahi tono i roto i te Rōpū. Hei rangatira mo te Ope o te Peninsula, i whakakaha ia i te Peninsula o Virginia ka wikitoria i te Pakanga o Big Bethel. I roto i te Peninsula Campaign, i whakamutua e ia te ope taua a McClellan o te Potomac i waho o Yorktown, e tuku ana ki a Maj. Gen. Joseph E. Johnston kia tae mai me nga whakapakari, ki te whakarite i te reti, me te tiaki i te taone nui o te Confederate, Richmond. I whakahētia a Magruder mō tana kaiārahi i ngā pakanga i Savage's Station
me Malvern Hill i te wā o te Pakanga o ngā Rā e whitu. I pau i a ia te toenga o te pakanga e whakahaere ana i te Takiwa o Texas, New Mexico, me Arizona me te Tari o Arkansas; i roto i tana mahi, i whakaarahia e Magruder te aukati moana i runga i Galveston ka riro ano i te taone i te tau 1863.