Chemical pesticides and their formulation ingredients can have unintended effects on microbes associated with plants and plant pests. These effects can be due to direct effects on the microbes or to effects on crops or weeds that subsequently affect the microbes. In addition to fungicides, some insecticides, herbicides, and formulation compounds are toxic to plant pathogenic microbes, as well as to potentially beneficial microbes, such as those that infect insect pests. These chemicals, especially herbicides, can also indirectly affect microbes through their effects on crops and weeds. For example, glyphosate strongly impairs shikimic acid pathway-based plant defenses to microbial diseases in glyphosate-susceptible plants, significantly increasing its efficacy as an herbicide. Some herbicides induce plant defenses against plant pathogens. For a complete understanding of integrated pest management and overall cost/benefit of pesticide use, much more information is needed on microbial/pesticide interactions.