The crime happened at Mima's Taste of Cuba near Irving Park Road and Richmond around 3:57 a.m.
The owner told ABC7 Chicago this is the second time they've been hit in a matter of months.
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In video shared with ABC7 Chicago, the burglars are seen jumping over the counter as they ransacked the store.
"Its frustrating," the owner of Mima's Taste of Cuba said. "You pay your taxes; you're trying to do the right thing out here and the criminals just keep... breaking into small businesses."
Video shows burglars ransack Mima's Taste of Cuba restaurant
The restaurant owner said the two suspects took off with $3,000.
"It's becoming almost a normal thing in the city of Chicago," the owner added.
Chicago police confirmed the robberies happened around 4 a.m. in the 2900-block of Irving Park Road.
The owner of the Cuban restaurant added that a neighboring Serbian restaurant called Cafe Beograd was also targeted.
Police said burglars broke in through a window and took a cash register.
Three suspects were seen driving off in a black car. No one is in custody.
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