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Probiotics are indispensable for maintaining the structure of gut microbiota and promoting human health, yet their survivability is frequently compromised by environmental stressors such as temperature fluctuations, pH variations, and mechanical agitation. In response to these challenges, microfluidic technology emerges as a promising avenue. This comprehensive review delves into the utilization of microfluidic technology for the encapsulation and delivery of probiotics within the gastrointestinal tract, with a focus on mitigating obstacles associated with probiotic viability. Initially, it elucidates the design and application of microfluidic devices, providing a precise platform for probiotic encapsulation. Moreover, it scrutinizes the utilization of carriers fabricated through microfluidic devices, including emulsions, microspheres, gels, and nanofibers, with the intent of bolstering probiotic stability. Subsequently, the review assesses the efficacy of encapsulation methodologies through in vitro gastrointestinal simulations and in vivo experimentation, underscoring the potential of microfluidic technology in amplifying probiotic delivery efficiency and health outcomes. In sum, microfluidic technology represents a pioneering approach to probiotic stabilization, offering avenues to cater to consumer preferences for a diverse array of functional food options.