Human urine, a highly saline solution rich in plant-available nutrients, leaves behind significant organic matter after nutrient recovery, necessitating additional treatment for environmental protection. While nutrient recovery from human urine is well-documented in the literature, research on the safe handling of the residual liquid phase is notably lacking. This study investigates nutrient recovery from source-separated human urine using clinoptilolite for the ion exchange/adsorption process and evaluates the safe management of the residual liquid through anaerobic granular sludge and a second-stage of sorption. The results indicated that the ion exchange/adsorption process, using an ammonium loading of 15 mg NH4+/g clinoptilolite, removed the majority of nutrients, achieving 82% ammonium removal and 100% phosphorus removal, along with 30% removal of organic matter. The residual liquid phase from the nutrient removal stage was treated separately with anaerobic digestion and a second-stage of sorption for further processing. Results showed that anaerobic processing removed 68%–84% of organic matter, with no additional nitrogen removal observed as expected, and produced 0.20–0.46 L CH4/L urine. The second-stage of sorption removed 59%–62% of organic matter and nearly all nitrogen. Both processes effectively removed organic matter, with sorption also eliminating nitrogen and anaerobic processing potentially generating biogas, making them recommended for improving the quality of the residual liquid phase before final disposal.