The cost of foodborne illness and food loss to the United States (US) economy is approximately $300 billion per year. This number monetarily quantifies the almost 10 million individuals who contract a foodborne illness and 141 trillion kcal of disposed food, enough to feed half the US population, each year. Despite the US having one of the safest and highest quality food supplies in the world, these figures illustrate the need to improve upon food safety and quality within the US supply chain and globally. Increasing consumer desires for minimally processed and clean label foods contributes to the challenge of addressing this need, as proven processing methods and food additives are being substituted or otherwise avoided/removed. To improve food safety and quality, food producers are seeking novel processing methods and additives to eliminate or kill foodborne pathogens and prevent the growth of spoilage microorganisms. Additional strategies to accomplish these goals include improvements to hygiene management within food processing facilities, and optimization of fermentation conditions or cultures as determined by an improved understanding of the microbial communities involved in commercial food fermentations. This dissertation presents examples of these strategies within the context of tools usage, namely adenosine triphosphate (ATP) monitoring of a food processing environment and next-generation amplicon sequencing of commercial tempeh and kombucha. The following studies demonstrate that the application of these tools is useful within the context of improving food product quality.