The present study investigated the effects of quinoa flour and inulin on some properties of cow milk kefir and goat milk kefir. In samples produced with both types of milk, inulin addition significantly (p < .05) increased viscosity and decreased syneresis. The lowest pH value was obtained in cow milk kefir produced with 0.5% quinoa flour at the end of storage period. Storage and various formulations of kefir samples had significant effects on the syneresis, viscosity, Streptococci and Lactobacilli counts, total phenolic content, antioxidant activity, titratable acidity and L*, a*, and b* values. Antioxidant activities in cow milk and goat milk kefir varied between 15.27 and 33.71 and between 9.00 and 20.45 (µmol Trolox Equivalent/L), respectively. Quinoa flour addition led to a decrease in the general appreciation score. The highest taste‐aroma and general acceptability scores were obtained with the sample that included 1% inulin in both milk types. Novelty impact statement Goat milk kefir exhibited lower total phenolic content and antioxidant activity when compared to cow milk kefir. Kefir with 1% inulin exhibited the highest Lactobacilli count at the beginning of storage. Inulin addition enhanced sensory properties, especially general acceptability and taste‐aroma scores.