Mycotoxin contamination is an important constraint to food security and public health in a range of food systems. Dietary exposure to mycotoxins is associated with health and nutrition adversities in humans and livestock. Surveillance systems and management strategies are rarely attentive to the specific needs and priorities of smallholder farmer communities, resulting in insufficient problem-solving capacity and poor adoption of effective intervention options. The aims of this dissertation were to understand the drivers of mycotoxin contamination in Indian smallholder food systems and to evaluate the utility of farmer research networks for connecting communities to locally meaningful and efficacious interventions. Novel insights into household-level aflatoxin B1 exposure risk were gained and a risk index was validated. Taking a food system-scale approach to surveillance, a range of crops were tested for several important mycotoxins across diverse Indian food systems over six seasonal time points. A model for participatory research in the context of a farmer research network (FRN) was implemented in six vulnerable communities, which designed and evaluated several pre- and post-harvest management strategies. In addition, I explored the host genetic determinants of symptom manifestation of the mycotoxigenic multi-fungal sorghum grain mold (SGM) disease complex. Several novel phenotypes of SGM symptom manifestation were developed and used to perform association studies. Candidate host genes underpinning fungal community composition in the disease complex were identified, yielding new insights regarding the contributions of mycotoxigenic Fusarium verticillioides to disease outcomes.