<p>In this study, MnFe₂O₄ magnetic nanoparticles were modified with the <i>Stenotrophomonas indicatrix</i> bacteria for the first time in the literature to develop an effective and novel bio-adsorbent for the remediation of toxic cationic dyes, specifically Rhodamine 6G (R6G) and Methylene Blue (MB), from contaminated aqueous media. MnFe₂O₄ and bacteria-loaded MnFe₂O₄ were thoroughly characterized using FTIR, XRD, and SEM-EDX analyses. XRD results confirmed that the cubic spinel structure of MnFe₂O₄ was preserved after bacterial modification, while FTIR spectra evidenced the successful incorporation of biological functional groups, including –NH, –OH, amide, and phosphate moieties, onto the nanoparticle surface. Adsorption performance of the dyes was evaluated in terms of parameters including aqueous solution pH, equilibrium time, bacteria-loaded MnFe₂O₄ dosage, and initial R6G and MB concentration. After investigating the effect of salt on adsorption efficiency, the applicability of the proposed adsorbent was assessed using real water samples. According to the experimental results, the optimum pH and equilibrium period for the uptake of both dyes were determined to be 8.0 and 60&#xa0;min, respectively. Kinetic analyses showed that the pseudo-second order kinetic model exhibited a superior fit in representing the adsorption rates of both dyes, while isotherm studies indicated that both Langmuir and Freundlich isotherm models fit the experimental data well. While the adsorption capacities of pure MnFe₂O₄ for MB and R6G were 19.5 mg g^− 1 and 15.3 mg g^− 1, respectively, these values reached 67.6 mg g^− 1 and 59.5 mg g^− 1 for the bacteria-loaded MnFe₂O₄. The obtained data revealed that bacterial modification significantly increased the adsorption capacity of MnFe₂O₄, suggesting that the developed bio-adsorbent stands out as an effective and promising candidate for the remediation of dye-contaminated effluents.</p> Graphical Abstract <p></p>