Microalgal-bacterial consortium can be used to upgrade biogas by removing CO2 and H2S. Photosynthetic biogas upgrading requires harvesting microalgal-bacterial biomass in order to use the biomass-free cultivation medium as scrubbing liquid in the absorption column. In this study, the efficiency of different flocculants (Zetag 8125, cationically modified cellulose nanocrystals, Tanfloc, chitosan, and FeCl3) to harvest microalgal-bacterial biomass used for biogas upgrading in alkaline medium (inorganic carbon concentration up to 1800 mg L−1 and a pH 10) was evaluated. Zetag and cationic cellulose nanocrystals resulted in maximum flocculation efficiencies of 95% (optimal dose 30 mg g−1) and 93% (optimal dose 20 mg g−1), respectively. Low flocculation was observed with other flocculants at doses as high as 200 mg g−1, which can be ascribed to the high pH of the alkaline medium. Zetag and cationic cellulose nanocrystals were selected for harvesting the biomass during semi-continuous cultivation of the microalgal consortium. Both Zetag and cationic cellulose nanocrystals were effective in flocculating the biomass with efficiencies of over 90% during five successive harvesting cycles. Gravity settling of the flocs formed by Zetag and cationic cellulose nanocrystals resulted in low biomass concentration factors of 7.7 and 2.0, respectively. Screening of flocs using a nylon mesh screen (pore size of 180 $m) resulted in a biomass concentration factor as high as 19.8. Zetag and cationic cellulose nanocrystals could be useful in harvesting biomass under high alkaline conditions without detrimental effects on biomass growth.