For nearly a century, human beings have been examining the use of soilborne biopesticides with an eye towards both reducing root diseases and increasing crop productivity. Throughout that long history, researchers have related the effects of microbial biopesticides to the ecological interactions among the applied antagonists, the targeted pathogens, and the crop host in the context of the crop production system. Reductionist approaches have revealed much about the individual components and the mechanisms by which they can contribute to plant health promotion. Such work is essential and must continue so new active ingredients can be discovered and vetted as inputs. However, it is also essential to step back once again to consider the degree to which we can successfully integrate various types of biopesticides into different production systems. Now, in the 21st century, a rapidly expanding market of organic, biological, and chemical-intensive farmers aims to use microbial biopesticides more widely and more successfully. To do so, we all need to better understand and manage the ecology of the cropping systems into which biopesticides are to be applied. For soilborne biopesticides, several challenges to successful delivery and some possible solutions for enhancing crop responsiveness will be discussed.