BACKGROUND: The incidence of sun-exposure-related skin conditions, such as melanoma, is a gradually increasing and largely preventable public health problem. Simultaneously, the availability of mobile apps that enable the self-monitoring of health behavior and outcomes is ever increasing. Inevitably, recent years have seen an emerging volume of electronic patient-generated health data (PGHD), as well as their targeted application across primary prevention areas, including sun protection and skin health. Despite their preventive potential, the actual impact of these apps relies on the engagement of health care consumers, who are primarily responsible for recording, sharing, and using their PGHD. Exploring preferences is a key step toward facilitating consumer engagement and ultimately realizing their potential. OBJECTIVE: This paper describes an ongoing research project that aims to elicit the preferences of health care consumers for sun protection via app-based self-monitoring. METHODS: A discrete choice experiment (DCE) will be conducted to explore how healthy consumers choose between two alternative preventive self-monitoring apps. DCE development and attribute selection were built on extensive qualitative work, consisting of the secondary use of a previously conducted scoping review, a rapid review of reviews, 13 expert interviews, and 12 health care consumer interviews, the results of which are reported in this paper. Following D-optimality criteria, a fractional factorial survey design was generated. The final DCE will be administered in the waiting room of a travel clinic, targeting a sample of 200 participants. Choice data will be analyzed with conditional logit and multinomial logit models, accounting for individual participant characteristics. RESULTS: An ethics approval was waived by the Ethics Committee Zurich. The study started in September 2019 and estimated data collection and completion is set for January 2020. Five two-level attributes have been selected for inclusion in the DCE, addressing (1) data generation methods, (2) privacy control, (3) data sharing with general practitioner, (4) reminder timing, and (5) costs. Data synthesis, analysis, and reporting are planned for January and February 2020. Results are expected to be submitted for publication by February 2020. CONCLUSIONS: Our results will target technology developers, health care providers, and policy makers, potentially offering some guidance on how to design or use sun-protection-focused self-monitoring apps in ways that are responsive to consumer preferences. Preferences are ultimately linked to engagement and motivation, which are key elements for the uptake and success of digital health. Our findings will inform the design of person-centered apps, while also inspiring future preference-eliciting research in the field of emerging and complex eHealth services. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/16087.