While in Natchez, Towson joined a volunteer artillery outfit to accompany the first American governor of Louisiana, William C. C. Claiborne, to New Orleans.

Towson quelled an attempted mass desertion and quickly rose through the ranks until he finally commanded the Natchez Volunteer Artillery.

With American and British tensions escalating, Towson was appointed captain in the United States Army artillery on March 15, 1812.

While commanding relatively few artillery pieces, his batteries' discharges were so numerous that his position during the Siege of Fort Erie became known as "Towson's Lighthouse".

He was buried at Oak Hill Cemetery in Washington, D.C.[2] Towson was succeeded as Paymaster-General by Col. Benjamin Larned, who served in that post until his death in 1862.