Monitoring agricultural toxins such as mycotoxins is crucial for a healthy society. High concentrations of these toxins lead to the cause of several chronic diseases; therefore, developing analytical systems for detecting/monitoring agricultural toxins is essential. These toxins are found in crops such as vegetables, fruits, food, and beverage products. Currently, screening of these toxins is mostly performed with sophisticated instrumentation such as chromatography and spectroscopy techniques. However, these techniques are very expensive and require extensive maintenance, and their availability is limited to metro cities only. Alternatively, electrochemical biomimetic sensing methodologies have progressed hugely during the last decade due to their unique advantages like point-of-care sensing, miniaturized instrumentations, and mobile/personalized monitoring systems. Specifically, affinity-based sensing strategies including immunosensors, aptasensors, and molecular imprinted polymers offer tremendous sensitivity, selectivity, and stability to the sensing system. The current review discusses the principal mechanisms and the recent developments in affinity-based sensing methodologies for the detection and continuous monitoring of mycotoxins and pesticides. The core discussion has mainly focused on the fabrication protocols, advantages, and disadvantages of affinity-based sensing systems and different exploited electrochemical transduction techniques.