The gut microbiota plays a central role in host metabolism, immunity, and overall function and is therefore of value for studies in sports nutrition. However, aside from its beneficial functionalities, the gut also harbours a reservoir of antimicrobial resistance genes (ARGs), collectively referred to as the resistome. Athletes, due to their specialised eating patterns, routine supplement intake, and elite-level physical exercise, may exhibit distinct microbiota alterations that can influence ARG abundance and dissemination. This study examines the intersection of sports dietetics, gut microbiota patterns, and antimicrobial resistance, with an emphasis on the resistome as the missing link to athlete health and sports performance. High-protein, specialised diets, probiotics, and energy-enhancing nutraceuticals modulate gut microbial ecology, either favouring or disfavoring the carriage of ARGs. Advances in metagenomics and functional microbiomics indicate that exercise-induced enrichment of selected microbiota (e.g., Prevotella and Akkermansia species) may reshape the resistome landscape and influence infection susceptibility as well as antibiotic responsiveness. Furthermore, sport-specific stress factors, such as repeated minor infections, antibiotic use, and co-training settings, can enhance ARG transmission. Understanding the gut resistome in athletes not only enhances our understanding of microbiota–performance interactions but also underscores the importance of infection control, individualised sports nutrition, and pharmaceutical and biotechnological interventions. Modulating the gut resistome using functional foodstuffs, synbiotics, and probiotics, which are designed to act selectively on specific resistome constituents, holds promise for optimising performance while minimising the risk of antimicrobial resistance. Integrated microbiome–resistome surveillance in sports science can develop safer and more effective nutrition models for athletes.