Population pressures and the need to optimize the use of limited available land has led to increasing cropping affluence levels within the maize agro-ecologies in Kenya, and a shift from large to smallholder intensification and multiple cropping patterns. Using a geographic information system, this study relates cropping patterns, by area share, maize productivity and household incomes across maize agro-ecologies, with the purpose to establish a decision support system for optimizing land allocation and in priority setting for introduction of new technologies such as Bt maize varieties. Results show that land use patterns and maize productivity in maize farming systems differ between agroecological zones. The high potential areas experience high maize yields, with maize grown alongside major cash crops such as tea and coffee. In contrast, lowland coastal strip and lake Victoria region tend to grow drought tolerant tuber crops (such as cassava and sweet potatoes) alongside maize in appreciable land sizes. Similarly the dry areas grow drought tolerant legumes such as pigeon pea alongside maize. These low potential areas thus concentrate on meeting their subsistence food self-sufficiency needs, pointing at risk management strategies against drought and pests such as stem borer, unlike high potential areas with high value cash crops. Maize breeders should therefore consider insertion of Bt- genes in maize varieties that would achieve high production and which are also capable of safely growing side by side with crops that meet different food security conditions in different agro-ecological zones in Kenya.