Members of Candida species cause significant problems in medicine and in many industrial branches also. In order to prevent from Candida sp. development, essential oils are more and more frequently applied as natural, non-toxic, non-pollutive and biodegradable agents with a broad spectrum of antimicrobial activity. The aim of the research was to determine changes in morphology and metabolic properties of Candida albicans in the presence of thyme and tea tree oils. Changes of enzymatic activity of isolates were observed in the presence of both tested essential oils, and they were primarily associated with loss or decrease of activity of all enzymes detected for control. Furthermore, only for 3 out of 11 isolates additional activity of N-acetyl-β-glucosaminidase, α-mannosidase, α-fucosidase and trypsin was detected. Vivid changes in biochemical profiles were found after treatment with tea tree oil and they were related to loss of ability to assimilate D-xylose, D-sorbitol and D-trehalose. The main differences in morphology of isolates compared to the control strain concerned formation of pseudohyphae structures. Both examined essential oils caused changes in cell and colony morphology, as well as in the metabolism of Candida albicans. However, the extent of differences depends on the type and concentration of an essential oil. The most important finding is the broad spectrum of changes in yeast enzymatic profiles induced by thyme and tea tree oils. It can be supposed that these changes, together with loss of ability to assimilate saccharides could significantly impact Candida albicans pathogenicity.