Microalgal–bacterial consortia (MBC) and microalgal consortia (MC) were cultivated with primary and final treated wastewaters, respectively, using a fluidised carrier. This study determines the main factors and operations required for flocculating suspended MBC (SMBC) and MC (SMC) in cultures. The flocculated SMBC and SMC with good settleability require the detachment of thickened MBC or MC on the carrier and suppressed SMBC and SMC formation by the original MBC and MC grown in the culture. Flocculation was achieved by controlling the carrier and culture replacements. A carrier replacement ratio of 0.04 d−1 and a culture replacement ratio of 0.95 d−1 minimised the dissolved organic carbon (15.3 mg-C/L) and SMBC residue (7.3 mg/L). Thus, treating primary treated wastewater with MBC formed using fluidised carriers is a promising strategy, enabling the use of whole cells in MBC for renewable energy production.