Cheese ripening involves a number of biochemical processes, mainly of a proteolytic nature, which are initially triggered principally by milk-coagulating enzymes and, afterward, by microorganisms or enzymes of microbial origin. The proteolytic reactions affect, primarily, the synthesis of macro- and medium-molecular peptides from casein. In turn, the advanced proteolysis ends in the formation of short peptides and free amino acids. Further reactions may lead to the formation of nutritionally unfavorable biogenic amines. The present study aimed to determine changes in the contents of bioactive peptides (anserine and L-carnosine), free amino acids, and biogenic amines throughout the ripening of cheese models produced with the addition of Lactobacillus genus bacteria. The contents of amino acids varied considerably in the cheese models, depending on the bacterial strain added and ripening time. After five weeks of ripening, the total content of free amino acids in the cheese models ranged from 611.02 (a cheese model with Lactobacillus casei 2639) to 1596.64 mg kg−1 (a cheese model with Lb. acidophilus 2499). After the same time, the contents of the total biogenic amines in the cheese models with the addition of lactobacilli were lower than in the control cheese model (except for the model with Lb. rhamnosus 489). Anserine was detected in all cheese models (79.29–119.02 mg kg−1), whereas no L-carnosine was found over a five-week ripening period in the cheese models with Lb. delbrueckii 490 and Lb. casei 2639. After a five-week ripening, the highest total content of bioactive peptides was determined in the cheese models containing Lb. acidophilus 2499 (136.11 mg kg−1).