(1) Background: The synthesis of core-shell magnetic mesoporous nanoparticles (MMSN) from phase transfer process is usually performed at 100-250 mg scale. At the gram scale, nanoparticles without core or with multicore systems are observed. (2) Methods: Iron oxide core nanoparticles (IO) were synthesized through thermal decomposition procedure of -FeO in oleic acid. Phase transfer from chloroform to water was then performed in order to wrap IO with mesoporous silica shell through the sol-gel procedure. MMSN were then functionalized with DTPA, and used for the separation of metal ions. Their toxicity was evaluated (3) Results: The phase transfer pro-cedure was crucial to obtained MMSN at large scale. Three synthesis parameters were rigorously controlled: temperature, time and glassware. Homogeneous dispersion of MMSN at the gram scale was successfully obtained. After functionalization with DTPA, the MMSN-DTPA were shown to have a strong affinity for Ni ions. Furthermore toxicity was evaluated in cells, zebrafish and through seahorse metabolic assays, and the nanoparticles were found nontoxic. (4) Conclusions: We developed a method of preparation of MMSN at the gram scale. After function-alization with DTPA, the nanoparticles were efficient in metal ion removal and separation, fur-thermore, no toxicity was noticed up to 125 µg.mL-1 in zebrafish.