[1][2][3] He commanded a brigade in the Confederate Department of Mississippi and East Louisiana in December 1862 and January 1863.

[2][3][5] During the siege of Vicksburg, Thomas and his regimental staff occupied Planters Hall, a building which survives and is listed on the U.S. National Register of Historic Places.

[1] After his parole, he brought Lieutenant General John C. Pemberton's report on the fall of Vicksburg to Richmond.

[2][3][4] From September 1864 to May 26, 1865—with the exception of March 17, 1865, to May 10, 1865, when he commanded the division of Major General Camille Armand Jules Marie, Prince de Polignac, during the latter's trip to France seeking help for the Confederacy from Napoleon III—Thomas commanded a brigade[7] in Polignac's division in the Confederate Army of the Trans-Mississippi.

[1][2][3][5] Thomas moved to Waveland, Mississippi, where he had bought a plantation, in 1907 and died there on December 3, 1907.

[1][2][3] Allen Thomas was buried at Ascension Catholic Church Cemetery, Donaldsonville, Louisiana, in the family vault of his wife.