Sulfonated polymer-based materials, among heterogeneous catalysts, are frequently utilized in chemical transformations due to their outstanding chemical and physical durability. In this regard, a magnetic sulfonated melamine–formaldehyde resin (MSMF) catalyst was successfully prepared from a mixture of sulfonated melamine–formaldehyde and Fe₃O₄ nanoparticles in two steps. MSMF was used as a heterogeneous catalyst for the one-pot, three-component condensation of benzyl pyrazolyl naphthoquinones in water as a green solvent and 4-[(indol-3-yl)-arylmethyl]-1-phenyl-3-methyl-5-pyrazolones. The antimicrobial and antioxidant activities of catalyst, benzyl pyrazolyl naphthoquinones, and 4-[(indol-3-yl)-arylmethyl]-1-phenyl-3-methyl-5-pyrazolones were evaluated using agar disk-diffusion and DPPH assays, respectively. The antioxidant activity of the catalyst and 4-[(indol-3-yl)-arylmethyl]-1-phenyl-3-methyl-5-pyrazolones was found to be 75% and 90%, respectively. Furthermore, catalyst, benzyl pyrazolyl naphthoquinones, and 4-[(indol-3-yl)-arylmethyl]-1-phenyl-3-methyl-5-pyrazolones exhibited antimicrobial activity against Staphylococcus aureus and Escherichia coli. In conclusion, MSMF is a superior catalyst for green chemical processes, owing to its high catalytic activity, stability, and reusability.