The aim of this study was to determine the effects of temperature and supplementation with skim milk powder (SMP) on the microbial and proteolytic properties during the storage of cottage cheese. Cottage cheese was manufactured using skim milk with 2% SMP and without SMP as the control, and then stored at 5°C or 12°C during 28 days. The chemical composition of the cottage cheese and the survival of the cheese microbiota containing starter lactic acid bacteria (SLAB) and non-starter culture lactic acid bacteria (NSLAB) were evaluated. In addition, changes in the concentration of lactose and lactic acid were analyzed, and proteolysis was evaluated through the measurement of acid soluble nitrogen (ASN) and nonprotein nitrogen (NPN), as well as electrophoresis profile analysis. The counts of SLAB and NSLAB increased through the addition of SMP and with a higher storage temperature (12°C), which coincided with the results of the lactose decrease and lactic acid production. Collaborating with these microbial changes, of the end of storage for 28 days, the level of ASN in samples at 12°C was higher than those at 5°C. The NPN content was also progressively increased in all samples stored at 12°C. Taken together, the rate of SLAB and NSLAB proliferation during storage at 12°C was higher than at 5°C, and consequently it led to increased proteolysis in the cottage cheese during storage. However, it was relatively less affected by SMP fortification. These findings indicated that the storage temperature is the important factor for the quality of commercial cottage cheese.