The store is the tech giant's 26th location in Southern California, housed inside one of L.A.'s historic venues and featuring an art gallery in the basement.
Cook was seen on the crowded main floor of the store, posing for selfies with shoppers while others arrived for "Genius Bar" tech support appointments.
The restoration of the Broadway theater, originally built in 1927 and among the first in the city, marks one of Apple's most significant projects to date.
The venue was shuttered in 1988, leaving the space empty and unused for years. Apple collaborated with leading preservationists, preservation artists and city officials in an effort to thoughtfully preserve the theater's beauty.
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"To get here on the first day, I mean, look around. This is why you come here," customer Cesar Moreno said. "I didn't expect for Tim Cook to be show up, which was kind of an icing on the cake there, but the energy here and everything else -- it's pretty incredible and I wanted to be a part of it.
"It fits with the downtown community," Moreno added. "It's kind of like that art deco vibe, right? It's embracing its surroundings and it's beautiful."