Soil test based fertilizer application is a widely accepted methodology for improved nutrient management. However, its applicability is severely curtailed in the developing countries due to lack of infrastructure and high cost of implementation. This is particularly true in the South and Southeast Asian countries where the size of holdings is typically low. Under such situation, Geographic Information System (GIS) based fertility maps could be used as a fertilizer decision support tool. The current study showed that nutrient contents of farmers’ fields predicted from the fertility maps closely match actual soil analysis. Fertilizer recommendations based on GIS maps and actual soil test did not produce significant yield difference in a rice-potato-sesame cropping sequence, suggesting its suitability as a decision support tool. A 250 m grid sampling was found to be adequate to address variability in a red and lateritic soil and predictability of soil parameters did not differ significantly between 50, 100 and 250 m grid-based maps. This methodology provides a cost effective option of implementing improved nutrient management in large tracts of small scale farming system in Asia.