As the prevalence of diabetes is predicted to rise globally in the coming decades, the demand for sugar substitutes is expected to increase significantly. In this context, natural sweeteners have been receiving particular attention, as artificial sweeteners have been associated with obesity and cardiovascular disease. One natural sweetener is yacon (Smallanthus sonchifolius) ((Poepp. and Endl.) H. Robinson), which could play a prominent role due to its high fructooligosaccharides yield. Yacon is currently only a minor crop in Europe and there is little information available on the environmental and economic impacts of its various cultivation systems. These are especially affected by nitrogen fertilization levels and genotype selection. Thus, before the crop is introduced on a larger scale, it is expedient to identify the most sustainable cultivation system. The life-cycle assessment (LCA) and life-cycle costing (LCC) analysis of yacon cultivation systems conducted in this study revealed significant differences between yacon genotypes and found that a nitrogen fertilization level of 80 kg N ha−1 significantly decreased production costs and simultaneously led to a comparatively good environmental performance. The results indicated that, for the holistic evaluation of agricultural systems, it is crucial to assess both the economic and environmental performance of new crops.