The evaluation of consumer preferences is a fundamental aspect for cosmetic products development and marketing. Consumer preferences are the result of sensory, emotional, and cognitive responses to products. They have been traditionally studied with sensorial evaluation methods which are time-consuming and are based only on the explicit responses of users and trained panels. Recently, with the evolution of the technology of physiological sensors, they have emerged as possible tools to study customer preferences from their physiological and non-conscious reactions. However, there is currently no standard protocol or application guide explaining how to use them for the evaluation of customer preferences for cosmetic products. In response to the above, this article presents the main factors to propose such a protocol. We present the steps, the decisions to be made, the criteria and some application guide for the selection of the appropriate evaluation methods and statistical analysis according to the goal of the consumer preferences study. A protocol is proposed and tested for a case study: the evaluation of consumer preferences over two cosmetic creams with different textures. As conclusions, physiological sensors give complementary information to surveys about the preferences of customers, because they enable to follow in real time their physiological reactions to the product. However, not all physiological sensors are equally applicable, and individual analysis of each signal may be inconclusive. It is recommended to study sensor signals and survey results in an integrated manner, overall considering that preferences are the result of a systemic complex process (sensory, physiological, emotional, conscious).