Amino acids are key components of cheese matrices by determining many characteristics in mature cheeses. They participate themselves to cheese flavour, are involved in many metabolic pathways during manufacture, and possibly act as mediator in some of the interactions that occur between microorganisms. They accumulate in the cheese matrix as cheese ripening progresses. Thermophilic lactobacilli are involved in their production in hard cooked cheeses. Present work focuses on points that still remain unclear. At which period of cheese making do amino acids begin to accumulate in the matrix? How does look their dynamics of accumulation afterwards? Which microorganisms are involved in their accumulation? Does composition of the cheese matrix limit or favour their accumulation? Twenty-four cheeses were manufactured under a typical hard cooked cheese process and varied only by the combination of thermophilic lactic acid bacteria inoculated, including at the most Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. Total amino acids content, microorganism counts and pH values were determined in the core at 2 (moulding), 3, 4, 6, 8, 10, 12 and 24 h (before salting) of cheese making, and at 7 months of ripening. Statistical models were constructed to explain the variability in amino acid content. Accumulation of amino acids began already after moulding and was highly variable according to manufacture time, for each combination inoculated but also between combinations inoculated. At first, it depended only on the number of microorganisms and the three species inoculated were involved, and then it depended also on the composition of cheese matrix but only the lactobacilli were involved. The amino acid contents in ripened cheeses were within the range usually observed in hard cooked cheeses. The content in mature cheeses is highly and linearly correlated to the content in young cheeses before salting. These results, together with those on accumulation of both peptides and each individual amino acid, will allow having an accurate view of the proteolysis during the manufacture of hard cooked cheeses.