Industrial wastewaters display a complex and diverse range of physicochemical properties that are measured, studied, and treated by businesses and water service providers. Less frequently measured are the microbial communities in these wastes, despite possible implications for health, equipment maintenance, and the environment. This study aimed to assess the microbial communities of eighteen raw and discharge-ready wastewaters across eleven industrial sites to compare the microbial compositions of these wastewaters across different industry sectors, on-site treatment levels, and other wastewater components. The potential for variance in the biomethane yield, depending on microbial communities, was also measured. Using targeted sequencing, a unique taxonomy was identified, including genera linked to animals (Acetitomaculum, Lactobacillus, NK4A214, Prevotella, and Shuttleworthia), cooling water (Bosea, Legionella, Methyloversatilis, and Reyranella), and extreme conditions (Alkalibacillus, Geobacillus, Halorubrum, and Pyrobaculum). However, the compositions of the microbial communities were not found to be directly correlated to industry sector or on-site treatment levels, nor were they found to have a direct effect on the biomethane potential. However, the presence of certain individual taxa is linked to the methane yield and treatment status and may be explained in the context of physicochemical properties while serving as potential markers for identifying, improving, or developing on-site processes.