With the war commencing in 1861, and Mr. Logan assigned to the command of the 31st Illinois Volunteers, Mrs. Logan and daughter Mary (nicknamed "Dollie", 1858–1940) returned to Capt Cunningham's home at Marion. The Illinois troops having been ordered into camp at Cairo, Mrs. Logan joined her husband there. During the battle of Belmont, Mrs. Logan cared for the wounded soldiers as they were brought back from the bloody field. When the army entered upon the Tennessee River campaign, Mrs. Logan again returned to her home, but was soon shocked by the news from Donelson that her husband had fallen at the head of his charging columns, dangerously wounded. She hastened to the scene to care for her husband, a struggle between life and death. At Memphis, in the winter of 1862–3, Mrs. Logan again joined her husband, now a general, and remained there until he led his troops in the campaign which ended in the surrender of Vicksburg. During this time, and to the end of the war, Mrs. Logan remained at Carbondale, where, out of the General's salary, they had bought an unpretentious home. Upon his return from the war, General Logan was nominated by acclamation for Congressman-at-large. After his election, Mrs. Logan returned to Washington and became a prominent figure in Washington society. After his service in the United States House of Representatives, General Logan was elected to the United States Senate. At the time of his nomination for the vice-presidency with James G. Blaine, it was she who restrained the impetuosity of her husband, who would have scorned the nomination, and prevented any differences between the leaders of the party.
