Security video clearly showed the man's face during the stickup Monday, and a 23-year-old surrendered Tuesday on a preliminary charge of robbery.
The robber turned himself in after his mother spotted him in surveillance video that aired on CBS affilate WISH Monday night.
Police say the robbery took an unusual turn after the gunman came around the counter when the clerk starting crying and talking about God.
The man, identified as Gregory Smith, said he had a 2-year-old child to support and asked for prayers about overcoming his hardships.
Police say the man removed the bullet from his gun and gave it to the clerk before taking her cell phone and the money.
"This whole robbery deal was pretty strange. I've been on 27 years and never seen nothing like this," said IMPD Lt. Jeff Duhamell, according to the station.
"After his mother saw him, she contacted him and he basically turned himself in," said Lt. Duhamell.
Smith is being held without bond facing felony gun and robbery charges. Police said he was already on probation for theft, the station reported.