Several companies of the 20th were mounted and dispatched to different points across Mississippi to oppose cavalry attacks during Grierson's Raid in the spring of 1863.

Under the command of General Joseph E. Johnston, the regiment took part in the withdrawal to Jackson in July, which resulted in Union capture of the state capital.

During the spring of 1864, the Regiment was part of a Confederate force sent to Jones County, Mississippi to arrest deserters and combat anti-Confederate insurgents led by Newton Knight.

During these battles in Georgia and Tennessee the 20th Regiment took heavy casualties and was greatly reduced in strength.

In the final stages of the war, the Regiment was sent east to fight in the Carolinas campaign.