It happened in the area of Pacheco Boulevard and Adelaide Drive around 9:30 a.m.
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Sheriffs say the deputy fired only after the suspect drew on him first, but the man's girlfriend has a much different story.
Angelica Jorgensen was there and says her boyfriend did not shoot first.
"He was just running from them and they shot him," she said. "They tackled him. They murdered him."
Jorgensen went on to tell ABC7 that her boyfriend was trying to turn his life around, and that he's even written children's books and donated a portion of the proceeds to charity.
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In contrast, sheriffs say he had long rap sheet and fired on the deputy first, narrowly missing his head.
"The suspect fired one shot toward the deputy's head, the deputy pulled out his weapon, fired at the suspect as well," explained Jimmy Lee, spokesman for the Contra Costa County Sheriff's Department.
Lee says two deputies were in the area on another matter just after 9:00 a.m. this morning, when one spotted the suspect, who had an arrest warrant for evading police and resisting arrest in another county.
Lee said the suspect, a 41-year-old man from Discovery Bay, has had numerous contacts with police and gang affiliations in Contra Costa County.
RELATED: Suspect dead after officer-involved shooting in Contra Costa County
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"He's had extensive law enforcement contacts," said Lee, citing assault with a deadly weapon, gun, and drug charges.
"He's a good guy," said Melissa Payne, who told us her sister is the suspect's girlfriend. She doesn't buy the sheriff's department's claim that the suspect fired at the officer first.
"Of course they're going to say that," said Payne. "They say that all the time. Why didn't they just shoot him in his leg or something, why'd they have to shoot him in his head?"
The incident is under investigation and the officer involved has been placed on paid administrative leave.