Adept use of fertilizers is critical if sustainable development goal two of zero hunger and agroecosystem resilience are to be achieved for African smallholder agroecosystems. These heterogeneous systems are characterized by poor soil health mainly attributed to soil nutrient depletion. However, conventional methods do not take into account spatial patterns across geographies within agroecosystems, which poses great challenges for targeted interventions of nutrient management. This study aimed to develop a novel population-based farm survey approach for diagnosing soil nutrient deficiencies. The approach embraces principles of land health surveillance of problem definition and rigorous sampling scheme. The advent of rapid soil testing techniques, like infrared spectroscopy, offers opportune avenues for high-density soil and plant characterization. A farm survey was conducted on 64 maize fields, to collect data on soil and plant tissue nutrient concentration and grain yield (GY) for maize crops, using hierarchical and purposive sampling. Correlations between soil test values with GY and biomass were established. The relationship between GY, soil NPK, and the tissue nutrient concentrations was evaluated to guide the setting up of localized critical soil test values. Diagnosis Recommendation Integrated System (DRIS) indices for total nitrogen (N), total phosphorus (P), and total potassium (K) were used to rank and map the prevalence of nutrient limitations. A positive correlation existed between plant tissue nutrient concentration with GY with R2 values of 0.089, 0.033, and 0.001 for NPK, respectively. Soil test cut-off values were 0.01%, 12 mg kg-1, 4.5 cmolc kg-1 for NPK, respectively, which varied slightly from established soil critical values for soil nutrient diagnostics. N and K were the most limiting nutrients for maize production in 67% of sampled fields. The study demonstrates that a population-based farm survey of crop fields can be a useful tool in nutrient diagnostics and setting priorities for site-specific fertilizer recommendations. A larger-scale application of the approach is warranted.