In the European Union, various crop diversification systems such as crop rotation, intercropping and multiple cropping, as well as low-input management practices, have been promoted to sustain crop productivity while maintaining environmental quality and ecosystem services. We conducted a data analysis to identify the benefits of crop associations, alternative agricultural practices and strategies in four selected regions of Europe (Atlantic, Boreal, Mediterranean North and Mediterranean South) in terms of crop production (CP). The dataset was derived from 54 references with a total of 750 comparisons and included site characteristics, crop information (diversification system, crop production, tillage and fertilization management) and soil parameters. We analyzed each effect separately, comparing CP under tillage management (e.g., conventional tillage vs. no tillage), crop diversification (e.g., monoculture vs. rotation), and fertilization management (e.g., mineral fertilization vs. organic fertilization). Compared with conventional tillage (CT), CP was higher by 12% in no tillage (NT), in fine- and medium-textured soils (8–9%) and in arid and semiarid sites located in the Mediterranean Region (24%). Compared to monoculture, diversified cropping systems with longer crop rotations increased CP by 12%, and by 12% in soils with coarse and medium textures. In relation to fertilization, CP was increased with the use of slurry (40%), and when crop residues were incorporated (39%) or mulched (74%). Results showed that conversion to alternative diversified systems through the use of crop rotations, with NT and organic fertilization, results in a better crop performance. However, regional differences related to climate and soil-texture-specific responses should be considered to target local measures to improve soil management.