During the Civil War Winans was elected a member of the Maryland House of Delegates (the lower house of the state legislature) for the 1861 special sessions called to discuss the issue of secession, and was arrested twice due to his anti-Federal activities and speeches. On the day before the Baltimore riot of 1861, Winans moved a resolution "protest[ing] in the name of the people of Maryland against the garrisoning of Southern forts by militia drawn from the free States" and 'calling upon citizens of the state unite "to repel, if need be, any invader who may come to establish a military despotism over us." He was arrested shortly after the riot, was released, and elected again on April 24 as part of a States Rights ticket. Meanwhile, Winans' firm was reportedly preparing weapons and munitions for the defense of Baltimore against union troops. According to the American of April 23, "At the works of the Mssrs. Winans, the entire force is engaged in the making of pikes, and in casting balls of very description..." (Brown, 65). On May 14, one day after martial law was declared in Baltimore, Winans was again arrested while returning from a special session of the Maryland legislature in Frederick (the session in which the Maryland legislature considered, but ultimately rejected, secession). He was quickly released, after signing a "parole" guaranteeing his loyalty to the federal government. Winans' arrest, by Benjamin Butler's Federal troops, was one of the cases where Lincoln's emergency suspension of "habeas corpus" was employed. Winans' brief incarceration was not legally challenged, as it was in the case of Johns Merryman (Ex parte Merryman).