Police say they were called to the restaurant in the 1300 block of Walnut Street shortly after 11 p.m. on Saturday.
When they arrived, they found a 43-year-old man with a gunshot wound to the head.
He was taken to Jefferson Hospital, where he later died.
Investigators say the victim, who is unhoused, was allegedly causing a disturbance inside the IHOP. As he was being escorted out by security, he allegedly turned and spat on the security guard.
The guard, identified as Yahaira Melendez, 38, then allegedly shot the victim in the head.
Family members of Melendez said she is a mother of three boys, and has never been in trouble.
They sent a statement to Action News that read in part: "We are shocked and devastated by the tragic events that occurred at the IHOP while she was working security, but we know she would never harm anyone unless she had no other choice in order to protect herself or others."
People who work in the area were surprised to learn what happened.
"Escalation. Where was the escalation?" asked Karr Anderson, who works next door. "Security guards do need to know how to withhold. Restraint."
Police previously said it appears the victim was not armed.
Melendez is now facing a murder charge, as well as other related offenses.