This study is part of a project that aimed to better understand the role of small mammals in the maintenance of the tick-borne encephalitis virus at four different sites in Switzerland. Here we focused on the detection of three intracellular pathogens, Anaplasma phagocytophilum, Rickettsia spp., and Babesia spp., in field-derived ticks that detached from 79 small mammals. We analyzed 465 Ixodes ricinus larvae after their molt and 14 semiengorged I. trianguliceps that were feeding on rodents. No pathogen was detected in I. trianguliceps. In I. ricinus, the most frequently detected pathogen was Rickettsia spp. (7.3%). All Rickettsia spp. identified DNA belonged to R. helvetica except one DNA sample that was identified as R. monacensis. The prevalence of Babesia spp. reached 2.4% and identification at the species level revealed B. venatorum (1.7%) and B. microti (0.4%). A. phagocytophilum was not detected in I. ricinus that detached from rodents. To verify the absence of A. phagocytophilum at the four sites, additional questing nymphs collected at these sites were analyzed for A. phagocytophilum. This pathogen was detected at one site only, where 2% (2/100) of questing ticks were infected. Some of these emerging pathogens are described for the first time in molted larvae that fed on rodents. The presence of medically relevant pathogens, with a global prevalence of 9.9%, highlights the importance to inform the medical corporation on the risk for human health in these areas.