Abstract Mesoporous silica MCM-41 was synthesized hydrothermally and then impregnated by different transition metals (such as Cr, Cu, Fe and Zn). The modified materials in calcined and non-calcined forms were tested in the adsorption of OG and MB dyes in single and binary system. Effect of calcination, contact time, initial dye concentration and adsorbent mass were studied. Two kinetics models were applied the first and the second order kinetics as well as the Freundlich and Langmuir isotherms were tested. The obtained samples were also used as anti-bacterial and anti-fungal agents using gram negative (P.aeruginos and E coli), gram positive (B. cereus, and S. aureus) pathogenic clinical bacteria and pathogenic fungi (Candida albicans). The result confirms that the adsorption process of both dyes follows second-order kinetics and their equilibrium data were fitted well to the linear Langmuir model. The maximum adsorption capacity of OG and MB dyes was 200 mg/g and 166 mg/g for non-calcined and calcined Zn/MCM-41, respectively. The adsorption of a binary mixture showed that the both materials are selective. The best selectivity was obtained by non-calcined Zn/MCM-41 wherein the OG dye was predominantly adsorbed. The application of all samples as anti-bacterial and anti-fungal agents showed encouraging results, but the best results were obtained by non-calcined materials, particularly with Cu/MCM-41 and Zn/MCM-41.