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. 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. He appeared to be her Confederate Secret Service "handler" during the formative phase of Confederate intelligence.