The goal of this study was to determine changes in contents of free amino acids, biogenic amines, and bioactive dipeptides (anserine and L-carnosine) in cheese models produced with the addition of nisin-producing strains of Lactococcus lactis over their ripening period. After 5 weeks of ripening, contents of total biogenic amines in the cheese models with the addition of L. lactis strains were lower than in the control cheese model. The cheese models examined differed significantly in contents of free amino acids through the ripening period. Individual free amino acids, such as ornithine, were found in some of the cheese models, which is indicative of their specific microbial activities. Both anserine and L-carnosine were detected in all variants of the cheese models. After 5-week ripening, the highest total content of bioactive dipeptides was determined in the cheese models produced with the nisin-producing culture of L. lactis 11454 (142.15 mg∙kg−1).