The second lieutenant of Company H resigning, Powell was elected to fill the vacancy.

After a service of a few weeks with his company he was put in charge of the fortifications he had constructed, being retained in this post after the departure of his regiment.

In the early winter of 1861-62 he recruited a company of artillery, largely from loyal Missourians.
This company was mustered into service as Battery F, 2d Illinois Artillery, John Wesley Powell, Captain.

After drilling a few weeks he was ordered to proceed with his battery to Pittsburg Landing, Tennessee, where he arrived the latter part of March, 1862.

The battery took part in the battle of Shiloh, April 6th of that year, and during the engagement, as Powell raised his arm, a signal to fire, a rifle ball struck his hand at the wrist glancing toward the elbow.