Bonnet was born in Geneva, Switzerland, to a wealthy family. He initially studied law, but a strong interest in insects led him to the field of natural history, to which he eventually devoted himself. His important observations have helped scientists better understand the process of insect metamorphosis. Many of Bonnet's observations are contained in his Traité d'insectologie (1745), which remains his highest regarded work in the field of insect biology.

Bonnet's observations on parthenogenetic reproduction, which is procreation without fertilization from sperm, are considered of special importance. He studied the reproduction of aphids and had determined that a number of females delivered live offspring even though their eggs had never been fertilized.

There was a debate over whether this reproductive phenomenon signified offspring that were "pre-formed" prior to their delivery, or offspring that were epigenetically developed, meaning that they formed during gestation. Bonnet was convinced that parthenogenetic reproduction involved pre-formed offspring.

From insect metamorphosis and parthenogenetic reproduction, Bonnet turned to the study of botany, but his research was cut short by failing eyesight. Even blindness did not still Bonnet's keen intellect; he simply applied himself to a more accessible discipline--philosophy.