Wolbachia, a maternally inherited endosymbiont, can significantly influence the biology of its arthropod hosts, including Drosophila melanogaster. Its presence can confound experimental results. To overcome this challenge, we present a protocol for eliminating Wolbachia from Drosophila melanogaster and other fruit fly species using tetracycline antibiotics. By treating flies with tetracycline during development, we successfully eradicate Wolbachia from the host lineage, enabling precise and controlled experiments. This protocol provides a valuable tool for the Drosophila research community. Wolbachia researchers can also benefit from this protocol to compare Wolbachia-bearing and Wolbachia-free insects.