Honey bees (Apis mellifera) are essential pollinators but are facing numerous threats from such pathogens as Nosema spp., which disrupt gut function and colony health. The honey bee gut microbiota contributes to digestion, immunity, and defense; imbalances in this community can intensify disease outcomes. This study used a caged bee model to evaluate how propolis, a natural resinous compound produced by bees, impacts gut microbial composition, microbiota dynamics, Nosema infection severity, and survival. Propolis supplementation promoted the growth of beneficial bacterial genera, Bifidobacterium and Commensalibacter, while reducing the prevalence of opportunistic taxa. It also alleviated the negative influence of ethanol exposure on microbiota stability. Importantly, microbial diversity and structure were maintained more effectively in propolis-treated bees, even under infection stress. These findings highlight the potential of propolis as a natural therapeutic agent that supports microbial homeostasis and mitigates disease impacts in honey bees. By demonstrating the dual role of propolis in protecting both microbiota composition and host resilience, this research offers insights into sustainable strategies for enhancing bee health and combating colony losses.