The aim of this study was to investigate the efficacy of pea protein isolate–alginate capsules (PPCs) on probiotic viability during transit of the porcine gastrointestinal tract. A Lactobacillus reuteri ATCC 53608 isolate selected for rifampin plus streptomycin resistance (LRR) was encapsulated in a pea protein isolate and alginate (LRR–PPC) using an extrusion and cross-linking method prior to freeze-drying. An in vitro study in simulated gastric juice showed that encapsulation increased (P < 0.001) survival in strong acid. After incorporation into the diet of weaned pigs, LRR were recovered from feces and digesta by selective culture. Fecal shedding of LRR from pigs fed LRR–PPC was higher (P < 0.001) than from pigs fed nonencapsulated LRR. Viable LRR counts were not different in homogenized stomach contents; however, higher (P < 0.001) counts were observed in distal intestinal contents for pigs fed LRR–PPC. Probiotic encapsulation using pea protein–alginate matrix can protect bacteria during upper intestinal transit improving viability in the distal gut and permitting a broader range of sensitive bacterial species candidates for probiotic application.