Houston police officers found the man dead just after midnight at the warehouse on South Post Oak near Heatherbrook.
Investigators say the business owner confronted the man, and at some point opened fire.
It is unclear if the suspect was trespassing or possibly attempting to burglarize the location.
"At this point, we don't know the motive. It's too early in the investigation. We don't know if it's a robbery or a burglary at the location," Detective Jason Escobar said. "There's a lot of tools, a lot of vehicles. It's a pretty packed warehouse, so it's unclear what kind of business [it is], whether it's a resale shop or a mechanic location. [It is] unknown at this point."
The business owner stayed on scene until officers arrived and is cooperating with the investigation.
Police say no one else was hurt in the shooting. They're looking for surveillance video in the area and possible witnesses.