The regiment remained in State service about six weeks, when General Hardee was ordered to make transfer of the State regiments into Confederate service. In making these transfers, nearly all the regiments lost the equivalent of a company in those men who declined to re-enlist for confederate service and were subsequently discharged. The 7th Arkansas transferred with the loss of only 17 men who refused to re-enlist as "Confederate troops". Cpts. C.C. Straughan of Co. G, and Cpt. James F. Archer of Co. H retired, and were replaced by Cpt. Warner and Cpt. Blackburn, respectively. The 7th Arkansas was ordered to Pittman's Ferry, where it was drilled and disciplined by General Hardee in person until the last of August, when Hardee's brigade marched by land to Point Pleasant, MO on the Missouri River, and then traveled by steamboat to the Confederate stronghold at Columbus, KY. From Columbus the brigade moved to Bowling Green, KY, in October, where it was assigned to the division commanded by General Simon B. Buckner. Here, Col. Shaver was appointed to command a newly-formed brigade made up of the 7th and 8th Arkansas regiments, the 19th Tennessee, and a battalion of the 9th Arkansas. Shaver's Brigade remained at Bowling Green until February, 1862, when that place was evacuated. Shaver's brigade guarded the Confederate rear during this retreat, being shelled by the artillery of Buell's advance while the last trains of stores were being loaded. On leaving, Col. Shaver, by order of Gen. Hardee, burned the depot and took down the telegraph wires. It was during the worst month in that climate, with rain and snow and the thermometer at night below zero, when this retreat was made. The 7th was caused to stand at arms all night by a report that a large force of Buell's army was coming on its heels, which turned out to be Helm's Kentucky cavalry coming in his rear by an unexpected order of march. General A.S. Johnston, at Nashville, sent a message to Colonel Shaver that the enemy's cavalry was advancing on his rear. This was made known to General Wood, of Alabama, who had taken command of the brigade during the retreat. General Wood refused to wait for the rear guard, and for this reason Colonel Shaver applied for and secured a transfer of the 7th to Hindman's brigade.
The regiment reached Nashville ten days after the fall of Fort Donelson, and went there to Murfreesboro, where the remnants of Zollicoffer's command had gone into camp after the battle of Fishing Creek. From Murfreesboro the 7th went to Decatur and thence to Courtland, Alabama, and went into camp at Corinth, Mississippi to await the concentration of the Confederate armies to meet the federal advance through Tennessee. Then followed the battle of Shiloh, where Shaver commanded the brigade under General Hindman. The 7th Arkansas acquitted itself valiantly at Shiloh, suffering high casualties and being dubbed "the Bloody 7th" by General Hardee. The regiment returned to Corinth after the Confederate repulse at Shiloh, where it rested and refitted and participated in the defense of that railroad junction from April to June, 1862. Upon Bragg's assumption of command of the Army of Mississippi, the army moved out again in a campaign intended to regain lost ground in Kentucky. The 7th fought there at Perryville on October 8, 1862, but suffered such high casualties in the attack there that it was subsequently consolidated with the 6th Arkansas Infantry, with whom it continued to serve with the Army of Tennessee for the remainder of the war.
Officers: Col. Robert G. Shaver. Field Officers: Lt.Col. William R. Cain; Maj. (later Lt. Col.) John M. Dean; Col. D.A. Gillespie; Maj. J.A. Hill; Maj. James T. Martin; Maj. J.C. Macauley; Lt. Col. J. Rutherford; Lt. Col. (later Col.) Peter Snyder