This editorial introduces our Special Issue entitled “Improving Fertilizer Use Efficiency—Methods and Strategies for the Future”. The fertilizer use efficiency (FUE) is a measure of the potential of an applied fertilizer to increase the productivity and utilization of the nutrients present in the soil/plant system. FUE indices are mainly used to assess the effectiveness of nitrogen (N), phosphorus (P), and potassium (K) fertilization. This is due to the low efficiency of use of NPK fertilizers, their environmental side effects and also, in relation to P, limited natural resources. The FUE is the result of a series of interactions between the plant genotype and the environment, including both abiotic and biotic factors. A full recognition of these factors is the basis for proper fertilization in farming practice, aimed at maximizing the FUE. This Special Issue focuses on some key topics in crop fertilization. Due to specific goals, they can be grouped as follows: removing factors that limit the nutrient uptake of plants; improving and/or maintaining an adequate soil fertility; the precise determination of fertilizer doses and application dates; foliar application; the use of innovative fertilizers; and the adoption of efficient genotypes. The most important nutrient in crop production is N. Hence, most scientific research focuses on improving the nitrogen use efficiency (NUE). Obtaining high NUE values is possible, but only if the plants are well supplied with nitrogen-supporting nutrients. In this Special Issue, particular attention is paid to improving the plant supply with P and K.