Agriculture and food systems go hand in hand, so proper farm management is necessary for ensuring global sustainability and food security. The impact of agricultural practices on production is direct, affecting all stages from germination to post-harvest treatment. Farmers who adopt structured management practices tend to increase their yields and profitability. In recent years, research on nanobiosensors has gained notable relevance, since nanostructures of nanometer size present unique properties that distinguish them from regular versions. Nanomaterials are being tested as potential candidates for transducer coatings that can accurately detect picomolar levels. This study was carried out through a systematic review of the available and updated literature on the incorporation of nanobiosensors in agronomy and agriculture. Nanobiosensors can be applied pre- and post-harvest and are easily portable and low-cost; thus, they allow for rapid on-site assessment of crop and soil health and detect biotic and abiotic stresses, nutritional status, and the presence of contaminants and spoilage indicators. Moreover, early detection of damage can prevent crop losses and avoid yield losses caused by the impact of stress. The combination of these biological sensors with nanomaterials amplifies the signal, increasing sensitivity and reducing the detection limit. Being highly selective, they enable the early detection and management of anomalies in agricultural production. This study analyzes recent novelties and existing limitations and discusses the structure and types of nanobiosensors in terms of their application in the agricultural sector.