There is increasing evidence showing the important role of commensal microbiota on the fitness of the animals, from affecting nutrient metabolism and energy regulation, to supporting immune system and modulating behavior. While direct effects of commensal microbiota on host physiology are progressively understood, little is known about their trans-generational effects on animal performance. We addressed the gap by manipulating the commensals of parental fruit fly pest (the Queensland fruit fly-Bactrocera tryoni) using the germ-free model, then investigating the effects of commensal microbiota on the development of flies in both parental and offspring generations. We found that the developmental time and adult emergence rate were not affected by commensal manipulation, but the pupal production was significantly different between treatments whereby fewer pupae were observed from the germ-free treatment. Flies of control and reinfection treatments were heavier than flies of germ-free treatment at all life stages (larva, pupa, adult) in both generations, suggesting that the presence of commensal microbiota consistently support the body weight gain. Together, our results indicate that the commensal microbiota has the long lasting effect on the development of the animals.