The effect of high hydrostatic pressure (HHP; 200 and 400 MPa) treatment of whole and skimmed pasteurized cow milk before fermentation on quality parameters of kefir was studied. HHP treatment of milk resulted in kefir batches with significantly lower (p ≤ .01) values of aw than the control kefir batches produced from untreated pasteurized milk. HHP treatment also led to 1.28-fold lower values for elastic and viscous properties of kefir batches produced from whole milk in comparison to the control batch. Pressures of 400 MPa caused a decrease in lightness and color intensity for whole milk kefir but had the opposite effect for the skimmed kefir. Additionally, structural changes in kefir were evidenced through the study of the microstructure of kefir batches. Obtained results showed that HHP is an effective processing technology that could allow developing kefir with novel sensory and quality attributes and increased shelf life. Practical applications There is an increasing interest in the development of safe dairy products with high nutritional quality as well as with unique sensory characteristics. This paper offers relevant information about kefir processing as it provides insights into the particular effects that high hydrostatic pressure treatment of the whole and skimmed milk prior to fermentation has on the physicochemical properties of kefir.