Ticks are important vectors of a variety of pathogens affecting humans and other animals, but they also harbor numerous microorganisms whose role is still limitedly investigated. Ixodes ricinus harbors the endosymbiont Midichloria mitochondrii, which is localized in ovaries and in salivary glands. The bacterium is vertically transmitted and is present in 100% of wild adult females, while prevalence values drop after some generations under laboratory conditions. Molecular and serological evidences showed that M. mitochondrii molecules are transmitted to the vertebrate hosts by I. ricinus during the blood meal. Our work was focused on monitoring M. mitochondrii antigens and DNA in a vertebrate model after infestation with I. ricinus for a time-span of four months. Two groups of rabbits were infested with I. ricinus females, respectively from the wild (naturally infected with the symbiont) and laboratory strain (lab; considered devoid of M. mitochondrii after quantitative PCR investigations) and screened using molecular and serological assays at nine time points. M. mitochondrii presence was detected in rabbits infested with wild I. ricinus ticks, but surprisingly also in those infested with lab ticks, albeit at later time points. This result prompted a more sensitive molecular screening of lab ticks, which were found to harbor very low symbiont loads. Our results indicate that transmission of the bacterium occurs even at low bacterial loads, and that antibody response against M. mitochondrii antigens begins within one week post-infestation with wild I. ricinus. Circulating DNA was detected in the blood of rabbits belonging to both groups up to the end of the experiment, suggesting a replication of the symbiont inside the vertebrate host.