The Irish fighter is being charged with strong-armed robbery and misdemeanour criminal mischief, police said.
The alleged incident took place as the 30-year-old left the Fontainebleau Miami Beach hotel at 05:20 local time.
A police report says he knocked the phone out of the fan's hand, stamped on it then picked it up and left with it.
"The victim attempted to take a picture of the defendant with his cell phone. The defendant slapped the victim's phone out of his hand, causing it to fall to the floor," a police report said.
"The defendant then stomped on the victim's phone several times, damaging it. The defendant then picked up the victim's phone and walked away with it, depriving him of it. The defendant was located and arrested."
It added the alleged victim's phone was valued at $1,000.
In a post on social media following his release, McGregor said: "Patience in this world is a virtue I continue to work on. I love my fans dearly. Thank you all."