Due to their health-promoting effects, the probiotic applications of lactobacilli have been investigated. Aside from their basic cellular functions, the extracellular activities of probiotic lactobacilli influence their establishment and interaction with the host. Many extracellular proteins play important roles in bacterial colonization and survival in their host's gastrointestinal environment. In this study, we compared the exoproteome of three lactobacillus strains isolated from the gastrointestinal tracts of pigs and chickens, namely, Lactobacillus mucosae LM1, L. johnsonii PF01, and L. johnsonii C1–10. Extracellular proteins collected in the mid-logarithmic growth phase were identified and quantified using a Q Exactive™ Orbitrap mass spectrometer (MS). Of 99 total extracellular proteins, 83% belonged to L. mucosae LM1; L. johnsonii PF01 strains had fewer extracellular proteins. Enolase, which is involved in the glycolysis pathway and has moonlighting functions in the adhesion of probiotic bacteria, was found in the core exoproteomes of the three strains. The most abundant proteins of each strain were phosphoketolase in L. mucosae LM1, aggregation-promoting factor in L. johnsonii PF01, and levansucrase in L. johnsonii C1–10. The observed differences between these three exoproteomes in terms of cellular and molecular function elucidate the extracellular activities of these isolates.