Consumer demand for natural and clean label foods continues to grow. This study aims to measure consumers’ perceived naturalness of food ingredients and further to investigate factors affecting their acceptability. Yogurt was chosen as the focal food of interest. A total of 20 common yogurt ingredients within the categories of sugars, stabilizers/thickening agents, preservatives, and coloring agents were selected. An online survey was administered to 526 yogurt consumers in the United States to evaluate the degrees of naturalness, familiarity, and acceptability of the selected ingredients. The degrees of acceptability were rated again when information regarding the functionalities and sources was given. Socio-demographic information was also collected. Results showed that the perceived naturalness of the coloring agents and preservatives varied substantially within each category. In contrast, the selected sugars were perceived as more natural, while stabilizers/thickening agents were perceived as less natural. These findings suggest that food manufacturers may focus on stabilizers/thickening agents in clean label reformulations. Results also showed that providing information regarding ingredient source, but not functionality, improved acceptability for some ingredients. This finding carries implications in that food manufacturers may consider including source information on their ingredient lists, and that regulatory agencies may need to set further guidelines for providing information on food labels. Additionally, some socio-demographic factors, such as consumers’ age and their knowledge on food ingredients, seem to be linked to the perceived naturalness and acceptability of ingredients. Understanding the link between socio-demographic characteristics and the acceptability of specific ingredients may help food manufacturers to market their products to specific demographic groups.