Among human body fluids, serum plays a key role for diagnostic tests and, increasingly, for metabolomics analysis. However, the high protein content of serum poses significant challenges for nuclear magnetic resonance (NMR)-based metabolomics studies because it can strongly interfere with metabolite signal detection and quantitation. Although several methods for protein removal have been proposed, including ultrafiltration and organic-solvent-induced protein precipitation, there is currently no standard operating procedure for the elimination of protein from human serum samples. Here, we introduce novel procedures for the removal of protein from serum by the addition of nanoparticles. It is demonstrated how serum protein can be efficiently, cost-effectively, and environmentally friendly removed at physiological pH (pH 7.4) through attractive interactions with silica nanoparticles. It is further shown how serum can be processed with nanoparticles prior to ultrafiltration or organic-solvent-induced protein precipitation for optimal protein removal. After examination of all of the procedures, the combination of nanoparticle treatment and ultrafiltration is found to have a minimal effect on the metabolite content, leading to remarkably clean homo- and heteronuclear NMR spectra of the serum metabolome that compare favorably to other methods for protein removal.