Rickettsiae of the spotted fever group (SFG) are zoonotic tick-borne pathogens. Small mammals are important hosts for the immature life stages of two of the most common tick species in Europe, Ixodes ricinus and Dermacentor reticulatus. These hosts and vectors can be found in diverse habitats with different vegetation types like grasslands and forests. To investigate the influence of environmental and individual factors on Rickettsia prevalence, this study aimed to analyse the prevalence of SFG rickettsiae in ticks and small mammals in different small-scale habitats in central Germany for the first time. Small mammals of ten species and ticks of two species were collected from grasslands and forests in the Hainich-Dün region, central Germany. After species identification, DNA samples from 1098 ticks and ear snips of 1167 small mammals were screened for Rickettsia DNA by qPCR targeting the gltA gene. Positive samples were retested by conventional PCR targeting the ompB gene and sequencing. Rickettsia DNA was detected in eight out of ten small mammal species. Small mammal hosts from forests (14.0%) were significantly more often infected than those from grasslands (4.4%) (p < 0.001). The highest prevalence was found in the mostly forest-inhabiting genus Apodemus (14.8%) and the lowest in Microtus (6.6%), which inhabits grasslands. The prevalence was higher in D. reticulatus (46.3%) than in the I. ricinus complex (8.6%). Adult ticks were more often infected than nymphs (p = 0.0199). All sequenced rickettsiae in I. ricinus complex ticks were R. helvetica, and the ones in D. reticulatus were R. raoultii. Unlike adults, questing nymphs have had only one blood meal, which explains the higher prevalence in I. ricinus adults. Interestingly, habitat type did influence infection probability in small mammals, but did not in ticks. A possible explanation may be the high prevalence in Apodemus flavicollis and A. sylvaticus which were more abundant in the forest.