Whiteleg shrimp (Penaeus vannamei) is currently facing significant challenges related to severe disease outbreaks. As the importance of the host–microbiota relationship is being revealed, modulating this relationship has become a key strategy in disease management. Xylooligosaccharides (XOS)—short-chain sugar molecules—have been gaining attention for their potential health benefits in the prebiotics field. In this study, an XOS-rich extract from Salicornia ramosissima was incorporated into shrimp feeds to evaluate its impact on gut health, with the main focus on gut proteomics and microbiota. XOS were incorporated at 0.1% (XOS_0.1) and 1% (XOS_1) concentrations, and a 14-day feeding trial, followed by a bacterial challenge with Vibrio harveyi, was performed. The effects of XOS were evaluated by assessing zootechnical parameters, gene expression in the hepatopancreas, and gut microbiota and proteome. The results showed no significant differences in zootechnical parameters and gene expression after the 14-day trial between animals fed XOS diets and control. However, shrimp fed XOS_1 showed an increased diversity of the microbial communities in the gut when compared with those fed control. Also, known shrimp gut symbionts, such as Ruegeria, Leisingera, and Demequina, were significantly enriched in groups fed XOS after the feeding trial. XOS also modulated the regulation of proteins in the gut. Nevertheless, stressful conditions appear to alter the effects of XOS and the dynamics of gut bacteria. Further studies are warranted to understand the impacts of long-term inclusion of XOS extracts, especially on health-related parameters and disease resistance.