Carotenoids are a class of phytochemical compounds found in a variety of fruits and vegetables (F/V) and therefore, are commonly used as a biomarker for F/V intake. The Veggie Meter® is a non-invasive research-grade instrument that detects and quantifies carotenoids in the skin. To determine current practices and examine variability among users, a survey was administered to researchers using the device (n = 19, response rate = 35.8%) and variation in anatomical site preparation, calibration, number of measurements, measurement site, and documentation was observed. A protocol was developed in partnership with Veggie Meter® users to outline the preparation, calibration, and data collection procedures for using this device for research purposes. While many protocol conditions will benefit from additional validation, this standardized protocol supports the development of a universal data repository to establish usual observed ranges, with the ultimate goal of examining associations between skin carotenoid scores and diet-related health outcomes.