BACKGROUND: Food allergies and intolerances are increasing worldwide, and mobile phone apps could be a promising tool for self-management of these issues. OBJECTIVE: This study aimed to systemically search and assess food allergy or intolerance apps in app stores using the multidimensional Mobile App Rating Scale (MARS) to rate the objective and subjective quality and to identify critical points for future improvements. METHODS: This systematic search identified apps through the keywords "food allergy," "food intolerance," and "allergens" in English, Spanish, and Italian in the Apple App Store (iOS) and Google Play Store (Android). The inclusion criteria were a user star rating of ≥3 (of 5 stars) to limit the selection to the most highly rated apps; ≥1000 reviews as an indicator of reliability; and the most recent update performed up to 2017. Then, the apps were divided according to their purpose (searching for allergen-free "food products," "restaurants," or recipes in "meal planners") and evaluated on a scale of 1 to 5 points using the MARS in terms of (1) app classification category with a descriptive aim; (2) app subjective and objective quality categories comprised of engagement, functionality, esthetics, and information sections (Medline was searched for eligible apps to check whether they had been tested in trials); and (3) an optional app-specific section. Furthermore, the output and input features were evaluated. Differences between MARS sections and between app purposes and correlations among MARS sections, star ratings, and numbers of reviews were evaluated. RESULTS: Of the 1376 apps identified, 14 were included: 12 related to food allergies and intolerances that detect 2-16 food allergens and 2 related only to gluten intolerance. The mean (SD) MARS scores (maximum 5 points) were 3.8 (SD 0.4) for objective quality, highlighting whether any app had been tested in trials; 3.5 (SD 0.6) for subjective quality; and 3.6 (SD 0.7) for the app-specific section. Therefore, a rating ≥3 points indicated overall acceptable quality. From the between-section comparison, engagement (mean 3.5, SD 0.6) obtained significantly lower scores than functionality (mean 4.1, SD 0.6), esthetics (mean 4, SD 0.5), and information (mean 3.8, SD 0.4). However, when the apps were compared by purpose, critical points were identified: meal planner apps showed significantly higher engagement (mean 4.1, SD 0.4) than food product (mean 3.0, SD 0.6; P=.05) and restaurant (mean 3.2, SD 0.3; P=.02) apps. CONCLUSIONS: In this systematic search of food allergy or intolerance apps, acceptable MARS quality was identified, although the engagement section for food product and restaurant purpose apps should be improved and the included apps should be tested in trials. The critical points identified in this systematic search can help improve the innovativeness and applicability of future food allergy and intolerance apps.