Jonathan Madden pleaded not guilty to one count of murder and two counts of attempted murder.
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Alejandro Garcia-Galicia, 41, was working with his 19-year-old son at the fast-food restaurant near the intersection of Century and Avalon boulevards Saturday night when he was shot and killed.
Investigators said the shooting stemmed from an argument that started when Garcia's son allegedly refused to accept what appeared to be a counterfeit $20 bill from a customer at the drive-thru.
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Los Angeles Police Department Chief Michel Moore announced at a vigil held Tuesday evening that a suspect had been arrested.
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Madden was taken into custody Monday at his home in South L.A. by members of the LAPD Gang and Narcotics Division, police said.
He has remained behind bars since then, jail records show.
Madden -- who was ordered to be held in lieu of $4.15 million bail -- is due back in a Compton courtroom Feb. 9. A date is scheduled to be set then for a hearing to determine whether there is sufficient evidence to allow the case against him to proceed to trial.
City News Service contributed to this report.