Tungstophosphoric acid (H3PW12O40) supported on silica-coated magnetite nanoparticles has been prepared and used as a heterogeneous acid catalyst (Fe3O4@SiO2@HPW) in the condensation of benzaldehyde (B) with glycerol (Gly) for the production of cyclic acetals. Physicochemical techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectrometry (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and N2 physisorption were used to characterize the prepared catalyst. The effect of glycerol/benzaldehyde molar ratio (1/1 to 1/1.2), temperature (80–120 °C), and catalyst amount (1–5%) on glycerol conversion and the selectivity in main reaction products: benzoic acid, 2-phenyl-1,3-dioxolan-4-yl)methanol, 2-Phenyl-1,3-dioxan-5-ol, 2-phenyl-1,3-dioxolane, and methyl 2-hydroxy-3-phenylpropanoate was studied to evaluate the catalytic activity of the prepared Fe3O4@SiO2@HPW catalyst. The optimization of these process parameters was conducted using Box–Behnken design (BBD). Using the BBD methodology, the optimal parameters (120 °C, 1:1.15 glycerol: benzaldehyde, 5% catalyst) were determined, for a glycerol conversion of and cyclic acetals yield of 85.95% and 78.36%, respectively. The catalyst also exhibits excellent activity for glycerol acetalization with other aromatic aldehydes such as cinnamaldehyde, p-methyl-benzaldehyde, p-hydroxy-benzaldehyde, and vanillin.