Cover crops (CCs) are a promising and sustainable agronomic practice to ameliorate soil health and crop performances. However, the complex of relationships between CCs, the soil, and the plant nutritional status has been little investigated. In this article, for the first time, we critically review, under a holistic approach, the reciprocal relationships between CCs and the soil physical and hydraulic properties, microbial, and faunal communities, soil nutrient availability, and plant nutritional status in temperate climates. For each of these topics, we report the current state of understanding, the influence of CC management options and suggested strategies, thus including both fundamental and applied aspects. In addition, we provide a detailed focus on the history of CCs and a list of the main temperate CCs. Cover cropping is a helpful practice in improving the physical, chemical, and biological soil properties, optimizing nutrient use efficiency and reducing the dependency of crops on external supplies of nutrients. The interactions between CCs and the nutritional status of soil and plants are complex and dynamic. Their understanding could be useful to set up an appropriate and site-specific management of fertilization. Management options play a key role in developing an effective and context-specific cover cropping.