The present study aimed to assess the antimicrobial potential of microwave radiation against microorganisms isolated from diatomaceous earth, a by-product of the beer filtration process. To this end, waste diatomaceous earth from an industrial brewery was subjected to microwave radiation in a closed-chamber microwave reactor. A microbiological analysis was conducted to ascertain the presence of specific microbial groups on the diatomaceous earth prior to and following microwave treatment. The results of the tests demonstrated that microwave radiation had a pronounced antimicrobial effect on the microorganisms under investigation. Microwave treatment resulted in a time-dependent reduction of microbial abundance, with bacterial counts decreasing by 93.8–99.9% across increasing exposure times (15–60 s). The most pronounced antimicrobial effect was observed after 60 s of microwave exposure, reducing bacterial abundance to 205 CFU·g⁻¹ D.M. and leading to the complete elimination of yeast. Consequently, this study broadens the application of microwaves to the eradication of microorganisms from the porous structure of diatomaceous earth, and it offers a novel approach for stabilizing this brewery waste.