In the present study, algicidal bacteria cultivated in an aqueous medium were utilized as a surface modification agent to develop an efficient adsorbent for the removal of Microcystis aeruginosa. The modification considerably enhanced M. aeruginosa cell removal efficiency. Moreover, the introduction of bio-compounds ensured specificity in the removal of M. aeruginosa. Additionally, the cyanotoxin release and acute toxicity tests demonstrated that the adsorption process using the developed adsorbent is environmentally safe. Furthermore, the practical feasibility of the adsorptive removal of M. aeruginosa was confirmed through cell removal tests performed using the developed adsorbent in a scaled-up reactor (50 L and 10 tons). In these tests, the effects of the adsorbent application type, water temperature, and initial cell concentration on the M. aeruginosa removal efficiency were evaluated. The results of this study provide novel insights into the valorization strategy of biological algicides repurposed as adsorbents, and provide practical operational data for effective M. aeruginosa removal in scaled-up conditions. Display omitted •Bacterial bio-compound was utilized as surface modifier for cotton adsorbent.•M. aeruginosa adsorption rate of bio-compound modified adsorbents was increased.•Surface modification of bio-compound increased selectivity for M. aeruginosa control.•Operation factor in adsorption process using developed adsorbent was investigated.•Harmful algal blooms adsorption process using developed adsorbent was environmentally safe.