Pediococcus acidilactici is one component of the nonstarter lactic acid bacteria in cheese; however, there is limited information about the contributions of this species to cheese ripening and flavor development. For this study, model Tilsit-type cheeses and model Gruyère-type cheeses were produced using P. acidilactici FAM18098 as an adjunct. The adjunct did not influence the cheese manufacturing processes. The pediococcal log counts ranged from 7.0–8.0 cfu g-1 after 90 and 120 days of ripening. The comparisons of the amino acid profiles of the control cheeses with the cheeses made with P. acidilactici revealed that the strain produced ornithine, a result of arginine metabolization by the arginine deiminase pathway. Furthermore, P. acidilactici formed α-aminobutyrate—a nonproteinogenic amino acid—and alanine while simultaneously metabolizing serine and threonine. The analysis of the volatile compounds in the cheeses showed that higher acetate, 2-butanone, and 2-butanol levels and lower diacetyl levels were present in the cheeses produced with P. acidilactici than in the control cheeses. The study illustrates that P. acidilactici can influence amino acid metabolism in cheese; further, ornithine, α-aminobutyrate, and acetate can serve as indicators for the presence of this species.