Microscopic investigation was done to determine the effect of entomopathogenic fungi, Beauveria bassiana and essential oil of Cymbopogon citratus on different life stages of Musca domestica. Scanning electron microscopy investigation of fungal infected larvae showed sluggish movement, rigor, and failure of body to balance in water. Treated larvae also revealed varied level of cuticle shrinkage and extreme dehydration. Surface of B. bassiana infected pupae showed varied stage of mycelial growth, while the cadaver of adult fly was observed to have extensive fungal growth covering their entire body surface. The application of C. citratus oils on M. domestica larvae resulted in skin shrinkage, spinous cells proliferation and bleb formation, while the treated pupae showed high incidence of incomplete emergence and malformation in emerged adult flies. The current study establishes effect of C. citratus essential oil and B. bassiana infection on different life stages of M. domestica.