Background: The gut microbiota plays a key role in human health, and probiotics represent one of the main strategies for its modulation. Knowledge of probiotics among medical and dietetics students may influence their future clinical practice. Objective: To compare the knowledge and perceptions of probiotics among medical and dietetics students. Material and Methods: A cross-sectional study was conducted among 107 students of the Medical University of Bialystok (55 medical students, 52 dietetics students). A 34-item questionnaire was used (maximum score: 51 points). Analyses included the Chi-square test and the Mann-Whitney U test; p < 0.05 was considered significant. Results: Dietetics students achieved a higher overall score than medical students (median: 31 vs. 27 points; p = 0.005). They more often correctly identified the definition of probiotics (94% vs. 69%; p = 0.002), appropriate product labeling (77% vs. 44%; p < 0.001), and distinguished fermented foods from probiotics (65% vs. 20%; p < 0.001). Differences were also observed regarding strain specificity (65% vs. 22%; p < 0.001), SIBO (75% vs. 42%; p < 0.001), and selected clinical indications, including IBS, atopic dermatitis, acne, ulcerative colitis, and upper respiratory tract infections. Medical students more frequently reported recommending probiotics to others (73% vs. 48%; p = 0.009). Conclusions: The overall level of knowledge was low, with dietetics students outperforming medical students in key areas. The findings suggest a potential need for enhanced evidence-based education on probiotics at the Medical University of Bialystok.