Khoa is an indigenous, heat coagulated, partially dehydrated whole milk product obtained by heating, evaporation and desiccation at atmospheric pressure. Owing to its nutritive value and moisture content khoa serves as a favourable medium for the growth of microorganisms on account of the unsatisfactory practices followed in its production, handling and storage results in poor shelf life. Hence, this study is envisaged to identify the contamination of yeast in the khoa and air samples of khoa plant as it forms an important base for preparation of milk sweets which are an integral part of Indian food heritage. A total of 216 samples (108 air and 108 khoa samples) 36 each from three organized dairies and from different sections (vat section, package section and storage section) of khoa plants were collected aseptically and analysed for yeast contamination. Saccharomyces species was the predominant yeast (42.11% and 40%) followed by Candida sp. (31.58 % and 34.55%) found in both air and khoa samples. The other yeasts encountered were Rhodotorula sp. and Torulopsis sp. in both air and khoa samples. The present study suggests theneed for more strict preventive and control measures used to avoid pre and post process contamination in khoa as it forms the base material for a variety of traditional sweets.