This study evaluated the protective effects of coproducts from agroindustrial processing of the tropical fruits acerola ( Malpighia glabra L., ACE), cashew ( Anacardium occidentale L., CAS), and guava ( Psidium guayaba L., GUA) on the probiotics Lactobacillus paracasei L-10, Lactobacillus casei L-26, and Lactobacillus acidophilus LA-05 during freeze-drying and storage. The occurrence of damage to membrane integrity, membrane potential, and efflux activity of Lactobacillus cells after freeze-drying was evaluated by flow cytometry, and viable counts were measured immediately after freeze-drying and during 90 days of storage under refrigerated or room temperature conditions. Probiotic strains freeze-dried without substrate had the overall highest count reductions (0.5 ± 0.1 to 2.9 ± 0.3 log cycles) after freeze-drying. Probiotics freeze-dried with fruit processing coproducts had small cell subpopulations with damaged efflux activity and membrane potential. Average counts of probiotics freeze-dried with ACE, CAS, or GUA after 90 days of storage under refrigerated or room temperature were in the range of 4.2 ± 0.1 to 5.3 ± 0.2 and 2.6 ± 0.3 to 4.9 ± 0.2 log CFU/g, respectively, which were higher than those observed for strains freeze-dried without substrate. The greatest protective effects on freeze-dried probiotics were overall presented by ACE. These results revealed that ACE, CAS, and GUA can exert protective effects and increase the stability of probiotic lactobacilli during freeze-drying and storage, in addition to supporting a possible added-value destination for these agroindustrial coproducts as vehicles for probiotics and for the development of novel functional foods.