As early as 1860, he secretly began a pro-Southern spy network in Washington, D.C., that was particularly active in the period immediately after secession.

[1] In early 1861, Jordan passed control of the espionage network to Rose O'Neal Greenhow; however, he continued to receive and evaluate her reports after she was restricted to house arrest in August 1861 and imprisoned in Washington, DC in January 1862.

During the advance from Corinth, Mississippi, into Tennessee, he rendered valuable service in preparing the men for the Battle of Shiloh, where he was conspicuous in efficiently managing the flow of orders to and from the various corps commanders and their respective staffs.

When Beauregard was reassigned to the defense of Charleston, South Carolina, Jordan accompanied his long-time friend and mentor as chief of staff for that department.

Immediately after the Civil War, Jordan lived in Tennessee, where he published a critical review of the Confederate operations and administration in Harper's Magazine.

That same year, General Jordan, with his lengthy administrative and combat experience, was appointed as chief of staff of the Cuban insurgent army.

Extremely short of supplies, Jordan resigned from his Cuban post a month later and returned to the United States, ending his long military career.

Continuing his interest in writing, Jordan published numerous articles on the Civil War and became the editor of the Mining Record.