The potential of a mesophilic–thermophilic–mesophilic anaerobic digestion system was investigated with respect to improvement of both digestion and sanitation efficiencies during treatment of liquid cattle manure. The pilot plant produced a high methane yield from liquid dairy cattle manure of 0.24 m3 (kg VSfed)−1. Considering the low system loading rate of 1.4–1.5 kg VS (m3 d)−1, digestion efficiency compared to conventional processes did not appear improved. The minimum guaranteed retention time in the tubular thermophilic reactor was increased compared to a continuously stirred tank reactor. Levels of intestinal enterococci in raw liquid manure as determined with cultivation methods were reduced by 2.5–3 log units to a level of around 102 cfu/mL. This sanitizing effect was achieved both during mesophilic–thermophilic–mesophilic and thermophilic–mesophilic treatment, provided the thermophilic digester was operated at 53–55°C. A change in feeding interval from 1 h to 4 h did not significantly alter methane yield and sanitation efficiency. It was proposed that a two-stage, thermophilic–mesophilic anaerobic digestion system would be able to achieve the same sanitizing effect and equal or better digestion efficiency at lower costs.