In this study, a fully integrated potentiometric soil nitrate sensor array is presented for real-time, multi-depth monitoring of soil nitrate concentrations. The sensor array is fabricated on a 3D-printed structure that enables simultaneous measurements at multiple soil depths. Each sensor in the array operates on a two-electrode potentiometric configuration. The working electrode is composed of a poly (3-octylthiophene) and molybdenum disulfide nanocomposite, which facilitates ion-to-electron transduction, and a nitrate-selective ion-selective membrane to ensure specificity. The reference electrode is modified with single-walled carbon nanotubes and a polymeric membrane to enhance stability. The sensor array was validated for real-time nitrate detection in different soil conditions using three different plant species: corn, cowpea, and tomato. The results demonstrate the system’s effectiveness in continuous nitrate monitoring across different soil depths, which is crucial for assessing soil health and optimizing fertilizer use. The sensor demonstrates a sensitivity of −81.76 mV/dec and a limit of detection of 0.65 ppm. Accuracy was confirmed through comparison with a commercial nitrate sensor, showing a statistically significant correlation with an R² value of 0.89. Data acquisition was carried out using a custom-built electronic circuit, enabling continuous measurement over a 5-hour period in each soil type, during which soil moisture levels were gradually increased. The sensor array demonstrated high stability and reliability under dynamic environmental conditions, supporting its suitability for applications in agricultural fields.