The purpose of this study was to compare the effect of the presence of protozoa in the rumen of wild roe deer (Capreolus capreolus) on the bacteria composition and digestion rate of the main carbohydrates of forage. The research material involved rumen content and rumen fluid, which were collected in the autumn-winter season, from eight adult males of roe deer with an average body mass of 22.6 kg. The microscopic analysis demonstrated that there were only protozoa in 50% of the animals sampled. Qualitative analysis revealed the presence of protozoa belonging to the genus Entodinium. The density of protozoal population varied from 6.5 to 38.7 × 105/mL rumen fluid. The analysis of bacteria composition indicated that protozoa did not have an effect on bacterial diversity. Furthermore, the results of hydrolytic activity revealed that the fastest digestion of carbohydrates was for pectin, while the slowest was inulin. The pH and redox potential in the rumen varied from 5.9 to 6.1 and from −248.1 to −251.1 mV, respectively. In summary, the presence of protozoa in the rumen of wild roe deer does not have an effect on the bacterial population and has no effect on the digestion rate of carbohydrates in the rumen.