Background Probiotic Bacillus coagulans GBI-30, 6086 (BC30) has been shown to increase protein digestion in an in vitro model of the stomach and small intestine. Once active in the small intestine after germination, BC30 aids the digestion of carbohydrates and proteins. The extent to which BC30 administration may impact protein digestion and amino acid appearance in humans after protein ingestion is currently unknown. This study examined the impact of adding BC30 to a 25-g dose of milk protein concentrate on post-prandial changes in blood amino acids concentrations. Methods 14 males and 16 females (n = 30, 26.4 ± 6.5 years; 172.3 ± 10.8 cm; 78.2 ± 14.8 kg; 22.6 ± 7.2% fat) completed two supplementation protocols that each spanned two weeks separated by a washout period that lasted three weeks. Participants were instructed to track their dietary intake and ingest a daily 25-g dose of milk protein concentrate with (MPCBC30) or without (MPC) the addition of BC30. Body composition and demographics were assessed upon arrival to the laboratory. Upon ingestion of their final assigned supplemental dose, blood samples were taken at 0 (baseline), 30, 60, 90, 120, 180, and 240 min post-consumption and analyzed for amino acid concentrations. Results Arginine (p = 0.03) and Isoleucine (p = 0.05) revealed greater area-under-the curve (AUC) in MPCBC30 group compared to MPC. In addition, Arginine (p = 0.02), Serine (p = 0.01), Ornithine (p = 0.02), Methionine (p = 0.04), Glutamic Acid (p = 0.01), Phenylalanine (p = 0.05), Isoleucine (p = 0.04), Tyrosine (p = 0.02), Essential Amino Acids (p = 0.02), and Total Amino Acids (p < 0.01) all revealed significantly greater concentration maximum (CMax) in MPCBC30 compared to MPC. Finally, time to reach CMax (TMax) was significantly faster for Glutamine (p < 0.01), Citrulline (p < 0.01), Threonine (p = 0.04), Alanine (p = 0.02) in MPCBC30 when compared to MPC. Greater mean differences between groups for AUC and CMax in women when compared to the mean differences in men were found for several amino acids. Conclusion In concert with previous in vitro evidence of improved protein digestion and amino acid appearance, these results reveal that adding BC30 to protein sources such as milk protein concentrate can improve AUC, CMax, and faster TMax. Follow-up research should examine differences between gender and explore how aging can impact these outcomes. Retrospectively registered on June 11, 2020 at ClinicalTrials.gov as NCT04427020.