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Abstract Nutrition measurement has broad applications in science, ranging from dietary assessment, to food monitoring, personalized health, and more. Despite its importance, there are currently no tools that offer continuous cotracking of nutrients direct from food. In this study, the multiscale engineering of silk biopolymer‐interlayer sensors is reported for comonitoring of nutrients. By manipulating various nano‐ to mesostructural properties of such biosensors, sensors are obtained with programmable sensitivity and selectivity to salts, sugars, and oils/fats. Notably, this approach requires no specialized nanomaterials or delicate biomolecules. Programmable biosensors are further formatted for wireless readout and characteristics of these passive, wireless nutrient monitors are studied in vitro. As a proof of concept, the discrimination and comonitoring of salt, sugar, and fat content direct from real, complex foods such as milk, meat, soup, and tea drinks are demonstrated. It is anticipated that such sensors can be utilized in emerging dietary tools for applications across food tracking and human health. In addition, such strategies are expected in structural engineering of sensors to be adaptable to existing or emerging selective or partially selective sensors.