Abstract This study aims at improving the existing algal-based wastewater treatment technologies by overcoming some of the major drawbacks of these systems such as large required land area, culture contamination, and energy-intensive algal harvesting. The experiments were carried out in an open photo-sequencing batch reactor at a laboratory-scale for nearly 2 months. A specific strain ACUS00207 of the aeroterrestrial green microalga Klebsormidium nitens (Kützing) Lokhorst was used. The strain is native to Bulgaria and belongs to a species that has never been used before in suspended growth systems for wastewater treatment for phosphorus removal. The culture of K. nitens showed promising results: phosphorus removal rates ranging from 0.4 to 1 mg total phosphorus L−1 d−1, efficient settling properties, and resistance to culture contamination with native microalgae. On the basis of the observed phosphorus removal mechanism of biologically mediated chemical precipitation/phosphorus precipitation, an innovative working mode of the sequencing batch reactor is suggested for reducing the hydraulic retention time and the required land area.