The combined assessment of organic and fatty acid profiles in yogurt with the activity of different starter cultures is a key issue to identify the effect of SCT on the flavor and aroma characteristics of the final product. The organic acid profile in a fermented dairy food is an indicator of the metabolic activity of added bacterial cultures (Maragkoudakis et al., 2006). Vénica, Perotti, and Bergamini (2014) reported that there was difference between organic acid profiles of yogurt samples having similar population of starter cultures, which was attributed to the changes in matrix structure of yogurt. Moreover, organic acids play an important role as natural preservatives in yogurt and they also affect the final characteristics of the product and cell viability of probiotics (Shah, 2017). In this context, Cruz et al. (2013) stated that the diversity of proteolytic activity of probiotic cultures caused production of additional organic acids which leads to more complex yogurt structure. The effect of SCT on the distribution of organic acids in buffalo milk yogurt was not explained enough in the literature. Fatty acids have also important role in the organoleptic and nutritional qualities of milk products. Especially, short‐chain fatty acids are involved in developing the sensory quality of products (Beshkova, Simova, Frengova, & Simov, 1998). It showed that yogurt is a good source of n − 3 fatty acids and the change in fatty acids during cold storage depends on milk source (Serafeimidou, Zlatanos, Kritikos, & Tourianis, 2013). Jia, Chen, Chen, and Ding (2016) stated that fatty acid profile of goat milk yogurt strictly depends on amount of carbohydrates and the ratio of starter cultures. Naydenova, Iliev, and Mihaylova (2013) showed that yogurt manufacturing increased the C18:3 fatty acid percentage of the total fatty acids in comparison with the ratio in raw buffalo milk, while it decreased the omega‐6 to omega‐3 fatty acid ratio. However, the effects of processing conditions and cold storage on the fatty acids content of buffalo milk yogurt are not well described.