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The soil microenvironment greatly influences a plant’s ability to absorb nutrients and germinate. Sensing these changes in soil medium is critical to understand plant nutrient requirements. Soil being dynamic represents changes in nutrient content, element mobility, texture, water-holding capacity, and microbiota which affects the nutrient levels. These minor changes affect the plant in early growth and development and studying these changes has always been challenging. Microfluidics provides a platform to study nutrient availability and exchange in small volumes of liquid or media resembling plant microenvironments. Here, we have developed a novel microfluidic chip-embedded molecular imprinted sensor for sensing nitrate and phosphate in the media. For data acquisition and recording we have implemented a potentiostat controlled via a microcontroller allowing data storage and transfer via a long-range radio module (LoRA). The microfluidic device’s functionality was validated by germination of the legume crimson red and recoding the nitrate and phosphate levels in media for 7 d. The MIP-based sensor measures nitrate and phosphate, in the range from 1 to 1000 mM. The accuracy of detection for nitrate and phosphate showed 99% and 95% respectively. The chip coupled with MIP based sensor for nutrient analysis serves as a platform technology for studying nitrate and phosphate nutrient exchange and interaction. This chip in the future can be implemented to study plant deficiencies, drought resistance, and plant immunity.