Agriculture faces an array of interrelated problems that call for development of new and revision of existing cropping systems towards the multiple needs of the 21st century. Agro-ecological engineering approaches aimed at design and exploration of alternative land use systems at various scales may support the identification of appropriate land use options. Engineering approaches are based on mathematical representations of well-founded agro-ecological principles while taking into account available resources and prevailing land-related objectives. The goal of this paper is to contribute to the development of a formalized approach to engineer cropping systems at the land unit level that can be used as building blocks for systematic explorations of land use options at farm or regional scale. The approach for engineering cropping systems at the land unit level consists of three steps: (i) goal-driven design of cropping systems, (ii) quantification of biophysical production targets and (iii) definition of the optimal mix of inputs required to realize production targets. This paper describes the approach and illustrates it with examples from the Sudano-Sahelian zone of Mali. Explicit attention is paid to the required numerical tools and their application to analyze consequences of uncertainty in the performance of engineered cropping systems. Using numerical tools, uncertainty is made explicit with the aim to better manage or reduce it. Identification of uncertainty at the designer's desk allows taking uncertainty into account before applying engineered land use systems in regional model studies or testing such systems in practice. Problems related to the application of numerical tools are discussed, including the future role of agro-ecological engineering as independent discipline within agricultural science.