The hard tick,Ixodes ricinus, a main Lyme disease vector, harbors an intracellular bacterial endosymbiont.Midichloria mitochondriiis maternally inherited and resides in the mitochondria ofI. ricinusoocytes, but the consequences of this endosymbiosis are not well understood. Here, we provide 3D images of wild-type and aposymbioticI. ricinusoocytes generated with focused ion beam-scanning electron microscopy. Quantitative image analyses of endosymbionts and oocyte mitochondria at different maturation stages show that the populations of both mitochondrion-associated bacteria and bacterium-hosting mitochondria increase upon vitellogenisation, and that mitochondria can host multiple bacteria in later stages. Three-dimensional reconstructions show symbiosis-dependent morphologies of mitochondria and demonstrate completeM. mitochondriiinclusion inside a mitochondrion. Cytoplasmic endosymbiont located close to mitochondria are not oriented towards the mitochondria, suggesting that bacterial recolonization is unlikely. We further demonstrate individual globular-shaped mitochondria in the wild type oocytes, while aposymbiotic oocytes only contain a mitochondrial network. In summary, our study suggests thatM. mitochondriimodulates mitochondrial fragmentation in oogenesis possibly affecting organelle function and ensuring its presence over generations.