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Aims: The Mediterranean fruit fly (the medfly) causes major losses of agricultural fruits. Its microbiome is mainly composed of various Enterobacteriaceae that contribute to nutrient acquisition and are associated with the fly's development. Moreover, the performance of males produced by the sterile insect technique is improved by providing mass‐reared insects with specific gut bacteria. Bdellovibrio and like organisms (BALOs) are obligate predators of Gram‐negative bacteria that efficiently preys upon diverse Enterobacteriaceae, making it a potential disruptor of the fly's microbiome. We hypothesized that the fly's microbiome can be targeted to control the insect. Methods and Results: Inoculation of B. bacteriovorus as free‐swimming or encapsulated cells into gut extracts significantly reduced gut bacterial abundance, sustaining predator survival. Similar treatments applied to adult flies showed that the predators also survived in the gut environment. While addition of the predators did not affect total gut bacterial abundance and end‐point fly mortality, a shift in the gut community structure, measured by high‐throughput community sequencing was observed. Conclusions: The bacterial predator of bacteria B. bacteriovorus can prey and survive in vivo in the medfly gut. Significance and Impact of the Study: This study establishes the potential of BALOs to affect the microbiome of insect hosts. [ABSTRACT FROM AUTHOR]