The first mentions of Bardonnex, in the form Bardonay, is dated back to 1153.
The commune of Bardonnex includes the hamlets Charrot, Croix-de-Rozon, and Landecy. It formed in 1851 from the division of Compesières. Its population was 666 in 1860, growing to 2,094 in 2000.
Bardonnex has Roman remains, an early medieval cemetery, and the 15th-century church of Notre-Dame. It was part of the Bernese bailiwick, then Savoy, before joining Geneva in 1816.
Bardonnex had a thriving clay industry, with a major tile factory employing 300 workers in the 1950s.