Solid waste landfill leachate and sewage sludge samples were quantitatively tested for viable Enterocytozoon bieneusi, Encephalitozoon intestinalis, Encephalitozoon hellem, and Encephalitozoon cuniculi spores by the multiplexed fluorescence in situ hybridization (FISH) assay. The landfill leachate samples tested positive for E. bieneusi and the sludge samples for E. bieneusi and E. intestinalis. The effects of four sanitization treatments on the inactivation of these pathogens were assessed. Depending on the variations utilized in the ultrasound disintegration, sonication reduced the load of human-virulent microsporidian spores to nondetectable levels in 19 out of 27 samples (70.4%). Quicklime stabilization was 100% effective, whereas microwave energy disintegration was 100% ineffective against the spores of E. bieneusi and E. intestinalis. Top-soil stabilization treatment gradually reduced the load of both pathogens, consistent with the serial dilution of sewage sludge with the soil substrate. This study demonstrated that sewage sludge and landfill leachate contained high numbers of viable, human-virulent microsporidian spores, and that sonication and quicklime stabilization were the most effective treatments for the sanitization of sewage sludge and solid waste landfill leachates. Multiplexed FISH assay is a reliable quantitative molecular fluorescence microscopy method for the simultaneous identification of E. bieneusi, E. intestinalis, E. hellem, and E. cuniculi spores in environmental samples.