The Stone Bridge served the needs of the Confederate Army through 1861. On March 9, 1862, the Confederates evacuated their winter camps in Centreville and Manassas in anticipation of fighting closer to Richmond. On orders from General Joseph E. Johnston, the Confederate rear guard blew up the Stone Bridge to prevent its use by the Union forces that soon occupied the area.
Union Army engineers eventually constructed a temporary wooden span across Bull Run using the remaining bridge abutments. This bridge served Union General John Pope's army at Second Manassas, August 28-30, 1862. After suffering another costly defeat, Union forces used the Warrenton Turnpike bridge as their primary line of retreat. In the early hours of August 31, the bridge was again destroyed, this time by the Union rear guard.