The United States Department of Agriculture downgrades on the order of 17% of all Swiss cheese produced in the United States due to defects. Many of these defects are related to improper eye formation, number, distribution, or size; leading to an industry loss of over $69 million per annum. The microbiome in Swiss-type cheeses plays a significant role in eye development due to production of organic acids and gaseous emissions contingent on bacterial abundance and phenotype. The relationship between bacteria and the organic acids they produce leading to Swiss cheese defects can be correlated using Next-generation sequencing and high-performance liquid chromatography coupled with UV-Vis and mass spectrometry, respectively. From two processing facilities, Next-generation sequencing identified bacterial genera Lactobacillus and Propionibacterium to be associated with Split/cracked cheese defects, Clostridium sensu stricto 12, Propionibacterium, and Lactobacillus to be associated with Irregular Eye formation/distribution (or collapsed eye formation) defects in Swiss cheese. Also identified through Next-generation sequencing was the genera “Candidatus Berkiella”, Propionibacterium, and Lactobacillus to be associated with Blind defects in Swiss cheese. Chromatographic separation and identification of organic acids provided evidence that lower levels of acetic and propionic acids were found in the Split/cracked cheese samples; lower abundance of acetic, lactic, propionic and butyric acids were found in Blind cheese samples (while a higher abundance of citric acid was found); and lower concentrations of citric, acetic, and propionic acids were found in Irregular Eye Distribution samples. From these data, it can be concluded that Swiss cheese monitoring for bacteria in the genera Lactobacillus, Propionibacterium, Clostridium sensu stricto 12, and “Candidatus Berkiella” can be used as a predictor of three types of cheese defects before and during long storage times leading to inferior product resulting in losses to the processor while organic acid monitoring presented in this text suggests more optimization is required.