Due to the high nitrogen and phosphorus content, source-separated urine can serve as a major nutrient source for microalgae production. The aim of this study was to evaluate the nutrient removal rate and the biomass production rate of Chlorella sorokiniana being grown continuously in urine employing a short light-path photobioreactor. The results demonstrated, for the first time, the possibility of continuous microalgae cultivation in human urine. The lowest dilution factor successfully employed was a factor of 2 (50% v/v urine). Microalgae dominated a smaller bacterial population and were responsible for more than 90% of total nitrogen and phosphorus removal. With a light-path of 10 mm, a maximum volumetric biomass productivity as high as 9.3 g L−1 d−1 was achieved. The co-existing bacterial population removed up to 70% of organic pollutants from the urine at a rate of 1300 mg COD L−1 d−1. Enriching the urine with magnesium, adjusting the N:P molar ratio, and shortening the reactor light-path further increased the volumetric biomass productivity to 14.8 g L−1 d−1. The corresponding nitrogen and phosphorus removal rates were 1300 and 150 mg L−1 d−1, respectively. The subsequently produced biomass contained 43–53% w/w proteins and 16–25% w/w total fatty acids.