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Solid-liquid separation makes further treatment, reuse and disposal of anaerobically digested dairy manure easier. However, high concentrations of solids and and nutrients as well as long time-to-filter of anaerobically digested dairy manure present a challenge to cost-effective solid-liquid separation and treatment. This study operated a two-stage biofiltration system by batch mode for passive solid-liquid separation and treatment of anaerobically digested dairy manure. The 1st-stage pebble biofilters attained separation through filtration and evaporation. Filtration was completed in 7-32 d. Separation effectiveness was related with temperature, initial total solids concentration, and time-to-filter of digested dairy manure. The pebble biofilters removed solids, chemical oxygen demand, ammonia, and orthophosphate mainly through surface filtration and microbial decomposition. The pebble biofilters removed 88% of total solids, 63% of soluble chemical oxygen demand, 70% of soluble biochemical oxygen demand, 68% of ammonia, and 68% of orthophosphate. The 2nd-stage sand biofilters further removed 83% of suspended solids, 45% of soluble chemical oxygen demand, and 43% of ammonia via microbial decomposition and depth filtration during 1-week batch operations.