Rubuta ci gaba ga wannan sakin layi - Lokacin da yakin basasa ya fara a 1861, Magruder ya bar Union Army don karɓar kwamiti a cikin Confederacy. A matsayin kwamandan sojojin Peninsula, ya karfafa yankin Virginia Peninsula kuma ya lashe yakin Big Bethel. A cikin Kamfen na Peninsula, ya dakatar da Sojojin Potomac na McClellan a wajen Yorktown, yana ba Manjo Janar Joseph E. Johnston damar isa tare da ƙarfafawa, shirya koma baya, da kuma kare babban birnin Confederate, Richmond. An soki Magruder saboda jagorancinsa a yaƙe-yaƙe a tashar Savage
da Malvern Hill a lokacin Yakin Kwanaki Bakwai. Ya shafe sauran yakin yana gudanar da Gundumar Texas, New Mexico, da Arizona da kuma Ma'aikatar Arkansas; a lokacin da yake aiki, Magruder ya ɗaga takunkumin jirgin ruwa a kan Galveston kuma ya sake kama birnin a 1863.