Probiotics, such as Lacticaseibacillus rhamnosus, are essential to the food industry for their health benefits to the host. The Lcb. rhamnosus strain is susceptible to processing, gastrointestinal, and storage conditions. In this study, Lcb. rhamnosus strains were encapsulated by complex coacervation in a gum arabic/chitosan or gum arabic/trehalose/chitosan and cross-linked with sodium tripolyphosphate. The physicochemical properties (zeta potential, water activity, water content, and hygroscopicity), encapsulation efficiency, and probiotic survival under storage conditions and simulated gastrointestinal fluids were evaluated. The results showed that crosslinking improves the encapsulation efficiency after drying; however, this result was remarkable when trehalose was used as a cryoprotectant. Furthermore, the encapsulation matrix preserved the viability of probiotics during 12 weeks with probiotic counts between 8.7–9.5, 7.5–9.0, and 5.2–7.4 log₁₀ CFU g⁻¹ at –20, 4, and 20 °C, respectively. After 12 days of digestion in an ex vivo simulator, acetic, butyric, propionic, and lactic acid production changed significantly, compared to free probiotic samples. This work shows that encapsulation by complex coacervation can promote the stability of probiotic bacteria in storage conditions and improve the viability of Lcb. rhamnosus HN001 during consumption so that they can exert their beneficial action in the organism.