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Chia seed mucilage (CM), flaxseed mucilage (FM), and inulin (INL) were used as encapsulating agents to evaluate the possibility of increasing the survival of <i>Lactobacillus casei</i> var. <i>rhamnosus</i>, renamed recently to <i>Lacticaseibacillus rhamnosus</i>, after spray drying. Moreover, the viability of encapsulated <i>L. rhamnosus</i> was determined during the 250 day storage period at 4 °C. In a second stage, the conditions that maximized the survival of <i>L. rhamnosus</i> were evaluated on other probiotic bacteria (<i>Lactiplantibacillus plantarum</i>, <i>Bifidobacterium infantis</i>, and <i>Bifidobacterium longum</i>). Additionally, the viability of encapsulated probiotics during the 60 day storage period at 4 and 25 °C was evaluated. The conditions that maximize the survival of <i>L. rhamnosus</i> (90%) predicted by a face-centered central composite design were 14.4% w/v of maltodextrin, 0.6% w/v of CM, and 90 °C of inlet air temperature. Additionally, under these encapsulating conditions, the survival of <i>L. plantarum</i>, <i>B. infantis</i>, and <i>B. longum</i> was 95%, 97%, and 96%, respectively. The probiotic viability improved during storage at 4 °C but decreased at 25 °C. The highest viability values obtained for probiotics during spray drying and during storage suggest a thermoprotector effect of CM, which would ensure an optimal probiotic efficacy in the product, thus promoting its utilization in the food industry.