Hardee served in the Western Theater and quarreled sharply with two of his commanding officers, Braxton Bragg and John Bell Hood.

[3] Now serving under Winfield Scott, Hardee was wounded in a skirmish at La Rosia, Mexico (about 30 miles (48 km) above Matamoros) in 1847.

Hardee operated in Arkansas until he was called to join General Albert Sidney Johnston's Army of Central Kentucky as a corps commander.

[3] Johnston was killed at Shiloh and Hardee's corps joined General Braxton Bragg's Army of Tennessee prior to the Siege of Corinth, Mississippi, until Department Commander P.G.T.

Beauregard was replaced by Bragg, who subsequently moved his army to Chattanooga before embarking on his Confederate Heartland Offensive into Kentucky.

In arguably his most successful battle, at the Battle of Stones River that December, his Second Corps launched a massive surprise assault upon the right flank of Maj. Gen. William Rosecrans's army, driving it almost to defeat, but again, as had happened at Perryville, Bragg failed to follow up his tactical success, opting instead to withdraw before the arrival of Union reinforcements.

After the Tullahoma Campaign, Hardee lost patience with the irascible, retreating Bragg and briefly commanded the Department of Mississippi and East Louisiana under General Joseph E. Johnston.

During the Chattanooga Campaign in November 1863, Hardee's Corps of the Army of Tennessee was defeated when Union troops under Maj. Gen. George Henry Thomas assaulted their seemingly impregnable defensive lines at the Battle of Missionary Ridge.

Following Sherman's withdrawal to Vicksburg, Hardee was once again sent back to Georgia, where he joined Johnston's army for the Atlanta Campaign.

As Johnston fought a war of maneuver and retreat against Maj. Gen. William T. Sherman, the Confederacy eventually lost patience with him and replaced him with the much more aggressive Lt. Gen. John Bell Hood.

After the Battle of Jonesboro that August and September, he requested a transfer and was sent to command the Department of South Carolina, Georgia, and Florida.