Since 1992, 74% of the plant protection products have been removed from the European market. While this process resulted in the withdrawal of most of the pesticides applied to the soil, alternative nontoxic solutions to these chemicals are lacking. Clearly there is an acute need for biorational control strategies for the management of soil pathogens and pests. Here we review the use of compost, biofumigation, and bacterial biological control. While these measures were first intended for sustainable and organic agriculture, we believe they will be adopted in the near future by the conventional sector. The pathogen- and pest-suppressive capability of composts is associated with microbial activity of bacterial and fungal populations in the rhizosphere and the interactions between microbials and macrobials in the soil. Biofumigation is a cultural method to treat soilborne pathogens and pests, using green manures, as well as by crop rotation, intercropping, and pure compound amendments as seed meal, dried plant material, or soil mulching. Biofumigation technology demonstrates the potential to reduce environmental pollution through the replacement of toxic synthetic pesticides with biodegradable plant secondary metabolites. While there is considerable literature on the use of biofumigation on soil pathogens and nematodes, much less can be found on the control of soilborne insect pests. Here the emphasis will be on field rather than laboratory experiments. We also present studies on the compatibility of biofumigation with natural enemies. Being a soil pathogen, Fusarium oxysporum is difficult to control, and Fusarium prevention is limited. Two groups of bacterial biocontrol agents for Fusarium wilt disease and Fusarium crown disease were investigated and developed: endophytic bacteria living within the plant and plant growth-promoting rhizobacteria (PGPRs) that colonize the rhizosphere. Here, we focus on the latter. Finally we conclude by presenting results from Israel using biofumigation for pathogen and pest control and hypovirulent isolates for the control of Fusarium wilt