The birds, named Monty and Rose, are both OK, but those who monitor the plovers saw a skunk reach into their enclosure and eat the eggs.
The Chicago Park District announced last month that three eggs had appeared in the birds' breeding grounds.
SEE MORE: Great Lakes piping plovers Monty and Rose lay eggs at Chicago's Montrose Beach
A couple years ago, the birds lost their nest, and days later built a second one.
Wildlife officials said they'll continue to monitor the birds.
This is their third year at Montrose Beach.