Inactivation of pathogens present in animal manure prior to land application has justified the use of advanced technologies. However, some alternatives are expensive or not effective due to the organic material and suspended solids present in the effluent (e.g., ozone, UV light). The use of hydrated lime (calcium hydroxide, Ca(OH) 2) is an attractive waste-water treatment option due to the ability of lime to kill pathogens and to extract phosphorus from manure at an alkaline pH. The present study aimed to evaluate the soluble phosphorus removal and pathogen inactivation (Escherichia coli, Salmonella enterica serovar typhymurium and Porcine circovirus type 2), in the liquid fraction and in the solid generated after Ca(OH) 2 addition in swine wastewater, exposed for 3 and 24 h at different pH conditions: 9.0, 9.5, and 10.0. The results showed the efficiency of pH elevation with Ca(OH) 2 in the removal of soluble P at pH 9.0 and the total inactivation of E. coli, Salmonella, and P. circovirus type 2 at pH 10.0. The liquid fraction (reuse water) could be safely used for cleaning the swine production facilities, and the solid fraction (precipitated P) could be used as a secondary product and fertilizer.