Meade fought against Virginians who threatened secession after the election of President Abraham Lincoln, preaching at Millwood against the looming civil war on June 13, nearly two months after Virginia's secession. Still, Meade believed in state's rights and acquiesced in his beloved Commonwealth's ultimate decision to secede. Although near retirement (John Johns having become his suffragan decades earlier), Meade became a leading figure in the Protestant Episcopal Church in the Confederate States of America. In 1859, shortly after John Brown's raid on Harpers Ferry (not very far down the historic Shenandoah Valley road from Meade's familial home and farm), the Episcopal Church held its General Convention in Richmond. There, the elderly Rt. Rev. Meade helped other southern bishops consecrate Henry Champlin Lay as a missionary bishop of the Southwest. Two years later, Bishop Meade as the senior seceding bishop, led the convention in Columbia, South Carolina in October 1861, which drew up the incorporation documents. However, he did not travel to Montgomery, Alabama for the preliminary organizational meeting July 3–6, 1861. Thus, Bishop Stephen Elliott of Georgia became the Presiding Bishop of the Confederate Episcopal Church.