High numbers of red deer (Cervus elaphus) pose a challenge for natural forests because of their high browsing intensities, especially during winter months. To mitigate this human–wildlife conflict, conservation management in Central Europe involves luring red deer into fenced winter-feeding sites. The supplementary diet provided in these so-called winter enclosures strongly differs from the natural diet of red deer. Dietary shifts, however, can lead to an imbalance of the gut microbiota, which could promote bacterial pathogens. Moreover, increased inter-individual contact in winter enclosures enhances the exchange of symbiotic but also pathogenic bacteria. In this study, we used high-throughput sequencing of the 16S rRNA gene in fecal samples of red deer inhabiting the Bavarian Forest National Park to investigate differences in the gut bacterial microbiota between individuals in winter enclosures and individuals that ranged freely in the forests in winter. We also investigated the occurrence of potential zoonotic bacterial pathogens in both study groups. Our results revealed that proportions of bacterial taxa, alpha- and beta-diversities, and relative abundances of amplicon sequence variants in the gut bacterial microbiota of the two groups differed. These differences were attributed to the enrichment of bacterial taxa involved in the digestion of the supplementary food and to different natural diets consumed before entering the winter enclosures. We detected sequences with high similarities to known red deer pathogens in both study groups, but their relative abundances were low, which suggests that the population of red deer of the National Park Bavarian Forest is healthy.