Matthews served as superintendent of contrabands for the Kansas Emancipation League starting in 1862. The League was an outgrowth of a school established for fugitive blacks in 1861. When word came that a force of blacks was to be raised, Matthews along with New England abolitionist
Ethan Earle wished to join the recruiting and be allowed to lead troops. He was initially told that he would not be allowed to lead and was offered a commission in the commissary or quartermaster department, but he protested. In August 1862, Senator
James Henry Lane acquiesced and authorized Matthews to raise a company for the
First Kansas Colored Volunteers and be its commander—and Matthews raised what would eventually be Company D. The regiment was originally mustered into the Kansas militia, and before being mustered into service in the Union Army they engaged in the
skirmish at Island Mound. This skirmish was the first time a regiment of black troops saw combat in the Civil War and occurred five months before the famous 54th Infantry conflict at the
Battle of Fort Wagner, in South Carolina. Matthews and his two lieutenants, Henry Copeland and Patrick Minor, were the highest-ranked black officers in the regiment but were denied commissions when the regiment became a part of the Federal Army. Each eventually was given commissions to serve in the Independent Kansas Colored Battery, where Matthews became commander of the Independent Kansas Colored Battery. and Andrew J. Armstrong replaced Matthews as captain of the company. In 1890, Williams testified that Matthews served in the organization and early drill of the company until May 1863. At an 1890 reunion of the First Kansas Infantry, Matthews was elected chairman of the gathering. In July 1864, Matthews and Minor were appointed recruiting officers for the
Independent Kansas Colored Battery out of Leavenworth, also called Douglas's Battery. In September he moved to Fort Scott to continue recruiting, mostly escaped Missouri slaves. Matthews and the battery were in Fort Scott during
Price's Raid, and local commander Colonel
Charles W. Blair put Matthews in charge of enrolling "all able bodied colored men in Bourbon County" and assembling them at the fort to defend them from Price. Price diverted towards the east, however. Matthews, Minor, and Captain
H. Ford Douglas were the only black artillery officers in the Union army. ==After the war==