The effectiveness of probiotics in delivering health benefits may be associated with their capacity to maintain a minimum concentration of 106 CFU/g during food storage and to successfully colonize the gastrointestinal tract (GI). Lacticaseibacillus rhamnosus (LR) is a probiotic that does not exhibit adequate stability under harsh conditions. To enhance the survival capacity of LR during gastrointestinal storage, alginate (ALG) was used as a primary encapsulating layer through extrusion microencapsulation. Subsequently, camelina seed mucilage (CSM) and camelina seed protein (CSP) were applied as secondary layers at varying concentrations (0%–4%). Among the tested formulations, ALG‐CSM‐CSP (1.5%, 4%, 4% w/w) exhibited significantly higher encapsulation efficiency (94.15%) and provided appropriate LR encapsulation in SEM image. Three saffron milk desserts (SMD) containing free LR (FLR), microencapsulated LR (MLR), and a control (C) were prepared, followed by physicochemical and microbiological assessments of the samples. The result showed that at the end of storage, SMD had the lowest pH (6.21), the highest acidity (30°D), and maintained the permissible limit of probiotic bacteria (6.7 log cfu/mL) among the samples. In GI, the MLR and FLR survival rates were 43% and 45.4%, respectively on the 14th day of storage, respectively. The MLR hardness (313.70 g), adhesiveness (2.01 mJ), chewiness (9.36) and gumminess (58.8) had the greatest values among the samples. Moreover, SEM images showed a relatively denser structure for MLR. In conclusion, this study highlights the potential of CSM and CSP to protect probiotics, offering valuable insights for developing new functional foods with improved survival during storage and GI.