Musca domestica Linnaeus (Diptera: Muscidae), a relevant synanthropic pest, is the most frequent dipteran species in farms and waste landfills. Insect Growth Regulators (IGR), insecticides with species-specific toxicity and low health and environmental impact, are known to act mostly on larval stages but may induce sterility in adults. We investigated the effects of diofenolan, an IGR analogue of juvenile hormone, on M. domestica, with special attention to female reproductive ability (egg-laying and hatching), and ovarian and ovariole morphology, using optical and transmission electron microscopy. We also tested the interactions between diofenolan and the activity of corpora allata, endocrine gland producing juvenile hormone required for ovarian development, by morphological and ultrastructural investigations. The results show that diofenolan negatively affects the reproductive ability of M. domestica, causing extensive morphological alterations in ovaries and ovarioles. In treated females, ovarioles showed nine different morphotypes that could be arranged into three “transformation paths”, and these alterations were able to reduce egg-laying. The effects of diofenolan on corpora allata, investigated at the optical and ultrastructural level in M. domestica, showed extensive alterations of the nuclei, cytoplasms, and mitochondria, strongly suggesting a rapid transition of the gland from inactivity to degeneration. The sterilizing effects of diofenolan in M. domestica are very interesting for integrated pest management programs within sustainable defence strategies against this relevant and annoying pest.