The small intestinal mucosa has the delicate task of allowing absorption of nutrients and limiting microbial colonization at the mucosal surface through production of antimicrobial peptides and proteins (AMPs). However, while environmental factors, including different diets, have been shown to alter AMP expression, the results from the literature are conflicting on their specific impact. Moreover, the interdependence between diet, AMPs, and metabolic health is largely unexplored. The aim of this study was thus to investigate the effect of obesogenic diets, obesity itself, and other variables, including mouse vendor, microbiota composition, and sex, on intestinal AMP expression. By using different dietary interventions in mice, we here show that prolonged intake of an obesogenic Western-style diet had a stronger impact on AMP expression than diet-independent obesity. Additionally, when comparing AMP expression under different diets in mice of both sexes from different vendors, the combined contribution of these factors had the strongest impact on absolute AMP transcript numbers, but also on the variability in small intestinal microbiota composition at the mucosa and content. Finally, we identified a novel host–microbe interaction, in which the gut commensal Faecalibaculum bloomed upon WSD-feeding and specifically induced the expression of the AMP Reg3g. Our findings thus reveal that the experimental setup, defined by mouse vendor, sex, and diet type, has a major influence on small-intestinal AMP expression. These findings could partly explain the discrepancy in the literature regarding the effect of diets on AMP expression, preventing any accurate generalization about the impact of diet on the antimicrobial response.