In this study, the effect of free and microencapsulation of Tragopogon Collins extract (TPE) on the properties of probiotic yogurt was investigated. For this purpose, first, TPE was extracted by ultrasound method. The amounts of phenolic and flavonoid compounds in TPE were 890.04 mg/g gallic acid and 512.76 mg/g extract (respectively), and it had high antioxidant and antimicrobial properties. Then, the extract was encapsulated by maltodextrin–whey protein concentrate. The results related to the particle size, zeta‐potential, and microencapsulation efficiency of the TPE microencapsulation were 93.87 nm, 18.99 MV, and 64.35% respectively. In order to investigate the effect of nano‐ and free TPE on the properties of yogurt during a 15‐day storage period of 5 treatments including control, nano‐ and free TPE at 750 and 1,000 ppm were provided and the physicochemical properties, probiotic bacteria viability, and sensory properties were investigated. The results showed that adding TPE to yogurt affects the physicochemical properties, probiotic bacterial viability, and sensory properties were investigated. The results showed that adding TPE to yogurt affects the physicochemical properties. TPE samples had lower pH, less syneresis, and more acidity, viscosity, and antioxidant properties compared to the control sample (p < .05). Furthermore, in these samples, the viability of probiotic bacteria during storage was higher than the control treatment and the sensory properties were acceptable. In most cases, better results were observed in nano‐TPE treatment. Therefore, by industrial production of probiotic yogurt containing nano‐TPE as a functional food, a new choice will be provided for consumers of dairy products that would have more desirable nutritional value and sensory properties.