All varieties of bean sprouts (mung bean, alfalfa, broccoli, and radish) are classified as a “super-food” and are common staples for health conscious consumers. Along with the proposed health benefits, there is also an inherent risk of foodborne illness. When sprouts are cooked, there is little risk of illness. The purpose of this dissertation was to explore novel techniques to minimize or prevent the incidence of foodborne illness associated with the consumption of sprouts. Three areas were investigated: 1) the use of a biocontrol organism, 2) the use of a novel spontaneous carvacrol nanoemulsion, and 3) the influence of the sprouting environment, antimicrobial treatments, and the presence of pathogens on the microbiota of sprouts. Using a novel strain of Serratia plymuthica, the growth of Salmonella spp. or E. coli O157:H7 were either suppressed or inhibited on sprouts that were co-inoculated with S. plymuthica and either pathogen. A novel carvacrol nanoemulsion was developed and tested for its efficacy against contaminated sprouting seeds and storage stability. The initial formulation was able to inactive low levels (≤ 3 log CFU/g) of S. Enteritidis or E. coli O157:H7 on mung beans, alfalfa, and radish sprouting seeds, but not broccoli. It was found that pH and high levels (≥10% v/v) of organic load significantly influenced the antimicrobial properties of the emulsion. With the addition of 50 mM acetic or levulinic acid, the treatment was able to inactivate 4 log CFU/g and 2 log CFU/g of pathogens on mung beans or broccoli seeds, respectively. The emulsion was found to be stable and still effective up to 30 days of storage at room temperature. Microbial population studies, utilizing a terminal restricted fragment length polymorphism analysis, showed that the microbiota differed between sprouting seed varieties. During the course of aseptic germination, there was a population shift which resulted in a less diverse population, mainly compose of Pseudomonadaceae. Sprouts that were commercially germinated had a more diverse population than aseptically germinated sprouts when seeds from the same distributer were used, suggesting that the sprouting environment can influence the final microbiota. The presence of pathogens resulted in a microbiota predominantly composed of Pseudomonadaceae and Enterobacteriaceae. Sprouting seeds that were treated with the carvacrol nanoemulsion resulted in a population comprised of mostly Pseudomonadaceae. Seeds that were initially contaminated with S. Enteritidis and treated with the carvacrol nanoemulsion had no detectable Salmonella restricted fragments or viable cells, suggesting complete inactivation of the pathogen. Sprouts will continue to a food for health conscious consumers. They will also be scrutinized for their chronic correlation with foodborne pathogens such as Salmonella spp. and E. coli O157:H7. It is vital that research continues in the areas of prevention, disinfection, and detection of pathogens on produce.