As a long time Chipotle fan (original Evans Ave. location FTW baby!!!), I always see this "OMG McDonald's OWNS Chipotle. McDonald's is the suck and this means Chipotle is the suck too DUCY?" argument. It's untrue, and Chipotle rules. (Not singling anyone out here, it just inevitably shows up in nearly every Chipotle thread.) The investment by McDonald's allowed Chipotle to expand outside of Denver, leading to the 100s of locations where you can partake in the deliciousness today.
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McDonald's Corp. has now fully divested its investment in Chipotle.
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Chipotle Wiki
Also, all locations are company owned, and not franchises.