A green-cheek conure and white-bellied caique valued at $1,700 total were returned to The Bird is the Word pet shop in Batavia Thursday morning.
The owner reported the baby birds missing Tuesday night.
Authorities believe the same individuals targeted a Naperville and Bolingbrook pet store the same night.
Charged with felony counts of retail theft are Erik Zalkus and Viviana Rossi, both of Berwyn, and Rebecca Cozzi, of Downers Grove. Charges are still pending against another man.
Early Thursday, authorities searched the Berwyn home of Zalkus and Rossi in the 3700-block of Gunderson. A Naperville Police press release says all the reported missing birds were found "in addition to other animals believed to have been stolen from other pet stores."