Anaerobic digestion (AD) is a commonly used method of processing waste. Regardless of the type of the used digestate (fertilizer, feedstock in case of solid-state fermentation, raw-material in case of thermal treatment) effective pathogen risk elimination, even in the case of high pathogen concentration is essential. An investigation of the survival time and inactivation rate of the Salmonella Senftenberg W775, Enterococcus spp., and Ascaris suum eggs during thermophilic anaerobic digestion performed on laboratory scale and confirmation of hygienization in full-scale operation were performed in this study. Except for sanitization efficiency, the AD process performance and stability were also verified based on determination of pH value, dry matter content, acidity, alkalinity, and content of fatty acids. The elimination of pathogen was met within 6.06 h, 5.5 h, and about 10 h for the Salmonella Senftenberg W775, Enterococcus spp., and Ascaris suum, respectively in the laboratory trials. The obtained results were confirmed in full-scale tests, using 1500 m3 Kompogas® reactors, operating in MBT Plant located in Poland. Sanitization of the digestate was achieved. Furthermore, the process was stable. The pH value, suspended solids, and ammonium content remained stable at 8.5, 35%, and 3.8 g/kg, respectively. The acetic acid content was noted between almost 0.8 and over 1.1 g/kg, while the concentration of propionic acid was noted at maximum level of about 100 mg/kg. The AD conditions could positively affect the pathogen elimination. Based on these results it can be found that anaerobic digestion under thermophilic conditions results in high sanitation efficiency.