The quality of fruits during storage depends on the storage environment and fruit microorganisms, since the activity of microorganisms can cause the decay of fruits. A correctly selected composition of gas mixture in a storage chamber extends shelf-life by reducing development of microorganisms, accordingly ensuring microbiological safety of fruits. The aim of the study was to evaluate the dynamics of microflora on the surface of apples within six months of cold storage that prior to storage had been treated with 1-methylcyclopropene (1-MCP), and those stored in ultra low oxygen (ULO) under different controlled atmosphere conditions. The highest microbial diversity and amount on the apple fruit surface was found when stored in cold storage. At the beginning of storage, 70% of the total surface microflora of fruits consisted of the following microscopic fungi: Penicillium spp., Alternaria spp., Botrytis spp., Aspergillus spp., Mucor genus and Cladosporium spp., bacteria from Bacillus genus, and yeasts like Candida curvata, C. fomata, Pichia etchellsii and P. carsonii. After three and six months of apple storage, partial microorganism inhibition was observed when comparing cold storage and cold storage + 1-MCP treatments, in turn, the most positive significant result was achieved when apples were stored under controlled atmosphere conditions. After six months of apple storage, the lowest amount of colony forming units (CFU) of bacteria, mould and yeast was estimated on the surface of apple fruits that had been stored using controlled atmosphere technique. Microorganisms, including Penicillium, Bacillus spp., Candida curvata, Pichia etchellsii and C. fomata were identified on the surface of ULO1 samples, while on ULO2 samples only Penicillium spp., Bacillus spp., C. curvata and C. fomata. After storage in controlled atmosphere, 90% of all microscopic fungi present on the surface of apples were yeasts.