Police were called to the 7-Eleven on Blackstone Avenue near Harvey Avenue around 9:30 a.m. Sunday.
Officers say an unhoused man, identified as 30-year-old Martin Carlos Aceves, had previously tried to steal from the store three weeks ago.
The clerk confronted Aceves and took him out of the store.
On Sunday, investigators say Aceves returned to the 7-Eleven and fired a gunshot.
Aceves then opened fire at the clerk, who was outside cleaning the station's gas pumps.
The clerk was not hit, but officers say a nearby empty car was struck.
Police arrested Aceves without incident at a nearby freeway embankment on charges of assault with a deadly weapon.