A Spirit Airline A319 in flight.
Misty Pinson, a spokesperson for Spirit, said "the flight crew received an indication of a possible mechanical issue. Following procedures, the crew declared an emergency and the plane returned to Chicago where it landed safely."
An FAA spokesperson told The Chicago Tribune a passenger noticed the missing covers, called cowlings, on the right side of the Airbus A319.
Pinson did not reveal how many passengers were on board the plane, but Spirit A319s typically seat 145.
Spirit says the cowling was recovered on airport property, and it is "actively investigating to confirm the specifics of what happened and the cause."
Flight 409 was bound for Fort Lauderdale, and passengers were rebooked or offered a refund, Pinson said.