The distribution of vegetative microbial cells and their spores in a supercritical CO2 extraction process was studied. The seed and flesh/skin fractions of the press residue of sea buckthorn berries (Hippophaë rhamnoides) from a juice factory were used as raw materials. A pilot-scale extraction plant was operated at 30 MPa at temperatures of 40 and 60°C. The number of yeasts, moulds and bacteria in the pulp/skin fraction, in the extraction residues, in the extracted oils as well as in the water phases separated from the extracted oils was estimated by the spread plate technique. The microbial content of the flesh/skin material was increased in some extractions by the addition of bacterial spores. In general, the extraction process led to a decrease in the bacterial count of the extracted material, whereas no microbial growth was detected in the oils extracted or in the water phases separated from them. Neither yeasts nor moulds were found in any samples after the extraction process. The microbial status of seed oil and flesh/skin oil obtained by industrial-scale CO2 extraction at 40°C and at 30 MPa before and after gelatine encapsulation remained unchanged. This proves that supercritical CO2 can be used to manufacture edible oil products free of living micro-organisms and their spores.