American Crystal Sugar Company (ACSC) factories have experienced periods of high unaccountable sucrose losses with consequent lower than expected recovery along with physical processing issues such as poor syrup filtration. Work is ongoing to identify the organisms involved and identifying metabolites associated with organisms identified. Analytical chemistry is more easily and rapidly obtained. In our studies we attempt to link specific organisms with various metabolites produced at a given set of processing conditions. We have found that under varying operating conditions a given organism can produce different metabolites that in turn impact the process differently. For instance, Leuconostoc may produce slime that interferes with filtration and settling under one set of conditions in another scenario a metabolite such as ethanol is produced with no physical manifestations, but an unaccountable loss is noted. Increased unaccountable losses have been correlated to increases in volatile fatty acids such as lactic acid, invert sugars, and ethanol in the diffusion juice and subsequent process streams. Elevated sucrose losses tend to occur when cossette ethanol levels increase along with invert sugars. The prior described events may or may not present as physical operating issues. The response to various treatments to manage undesirable microbial activity during the process can vary greatly. The essence of the studies completed is to define the relationships between microbes, environment, and metabolites produced.