Coagulation-based pre-treatment efficiency of high strength digestate of food waste (HSDFW) anaerobic digestion is negated by organic ligand-catalyzed decomposition of coagulants. In this study, an efficient HSDFW pre-treatment method, magnetic seeds (MS) coagulation, was employed by using highly stable Keggin Al30 nanocluster (PAC30), MS and polyacrylamide (PAM), and its operation was optimized by evaluating the performance of removing turbidity, total suspended solids (TSS), chemical oxygen demand (COD), and total phosphorous (TP) phosphate. Results showed that at the optimum dosage of 4.82 g/L, PAC30 demonstrated excellent removals as high as 98.93% ± 0.1% of turbidity, 98.04% ± 0.1% of TSS, 58.28% ± 0.3% of total COD, 99.98% ± 0.01% of TP and 99.50% ± 0.01% of dissolved phosphate, respectively. Apparent molecular weight (AMW) and three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy analyses demonstrated more efficient removal of dissolved organic matter (DOM), particularly non-biodegradable and hydrophobic components by PAC30 than commercial coagulant. The sedimentation was much improved from 40 min by coagulation/flocculation to about 5 min settling by MS coagulation. The PAC30 based magnetic coagulation (MC) presents theoretical guidance on a cost-effective and much less footprint pre-treatment alternative for high strength wastewater.