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<i>Wolbachia</i> are maternally transmitted intracellular bacteria that are not only restricted to the reproductive organs but also found in various somatic tissues of their native hosts. The abundance of the endosymbiont in the soma, usually a dead end for vertically transmitted bacteria, causes a multitude of effects on life history traits of their hosts, which are still not well understood. Thus, deciphering the host-symbiont interactions on a cellular level throughout a host's life cycle is of great importance to understand their homeostatic nature, persistence, and spreading success. Using fluorescent and transmission electron microscopy, we conducted a comprehensive analysis of <i>Wolbachia</i> tropism in soma and germ line of six <i>Drosophila</i> species at the intracellular level during host development. Our data uncovered diagnostic patterns of infections to embryonic primordial germ cells and to particular cells of the soma in three different neotropical <i>Drosophila</i> species that have apparently evolved independently. We further found that restricted patterns of <i>Wolbachia</i> tropism are determined in early embryogenesis via selective autophagy, and their spatially restricted infection patterns are preserved in adult flies. We observed tight interactions of <i>Wolbachia</i> with membranes of the endoplasmic reticulum, which might play a scaffolding role for autophagosome formation and subsequent elimination of the endosymbiont. Finally, by analyzing <i>D. simulans</i> lines transinfected with nonnative <i>Wolbachia</i>, we uncovered that the host genetic background regulates tissue tropism of infection. Our data demonstrate a novel and peculiar mechanism to limit and spatially restrict bacterial infection in the soma during a very early stage of host development. <b>IMPORTANCE</b> All organisms are living in close and intimate interactions with microbes that cause conflicts but also cooperation between both unequal genetic partners due to their different innate interests of primarily enhancing their own fitness. However, stable symbioses often result in homeostatic interaction, named mutualism, by balancing costs and benefits, where both partners profit. Mechanisms that have evolved to balance and stably maintain homeostasis in mutualistic relationships are still quite understudied; one strategy is to "domesticate" potentially beneficial symbionts by actively controlling their replication rate below a critical and, hence, costly threshold, and/or to spatially and temporally restrict their localization in the host organism, which, in the latter case, in its most extreme form, is the formation of a specialized housing organ for the microbe (bacteriome). However, questions remain: how do these mutualistic associations become established in their first place, and what are the mechanisms for symbiont control and restriction in their early stages? Here, we have uncovered an unprecedented symbiont control mechanism in neotropical <i>Drosophila</i> species during early embryogenesis. The fruit fly evolved selective autophagy to restrict and control the proliferation of its intracellular endosymbiont <i>Wolbachia</i> in a defined subset of the stem cells as soon as the host's zygotic genome is activated.