First in this chapter, we will enumerate overall microbial populations of plant protein using “Beyond Burger” as an example to use 3M petrifilm including aerobic plate counts (APCs), total coliform counts (TCCs), and generic Escherichia coli (ECCs). APCs, TCCs, and generic E. coli are recognized as indicator microorganisms, which are usually suggested to be a surrogate (non-pathogenic) to evaluate the presence of pathogens in that environment. APCs usually indicate the total aerobic microorganisms. TCCs are from the intestine of warm-blooded animals; are gram-negative, non-endospore-forming, facultative, fermentation lactose-generating acid and gas; and belong to the Enterobacteriaceae spp. Finally, generic ECC is a member of TCCs, and its presence indicates fecal contamination. 3M petrifilm plate is called a “paper medium” with a foam barrier accommodating a 20 cm2 circular plating surface covered with a top plastic film. It also has a cold water-soluble gelling agent containing dehydrated nutrients in the middle of the film for plating, incubating, and numerating indicator microorganisms. Second in this chapter, we will isolate Salmonella spp. and Listeria monocytogenes, and using a selective, enriched medium, immunology assay and multi-channel biochemistry test to confirm the presence/absence of these two foodborne pathogens.