The contact of nanoparticles with biological fluids such as serum results in rapid adsorption of proteins at the nanoparticle surface in a layer known as the “protein corona”. Protein coatings modify and control the behavior of the nanoparticles potentially altering the aggregation state and cellular response, which may influence their fate and hazard to human health. Cells are likely to interact with the protein interface rather than with bare surface; therefore it is important to study the protein layer and develop appropriate measurement tools. In this study we investigate how adsorbed proteins from serum affect the size and the surface charge of plain and aminated silica nanoparticles. Particle size and size distributions in buffer and serum-based biological media were studied using tunable resistive pulse sensing (TRPS), as well as differential centrifugal sedimentation (DCS) and dynamic light scattering (DLS). Average and single particle ζ-potentials (related to surface charge) were also measured by electrophoretic light scattering (ELS) and TRPS, respectively. Size measurements showed an increase in size of the nanoparticles upon acquisition of a protein layer, thus allowing an estimation of its thickness. DLS proved incapable of providing an accurate measurement of the nanoparticles’ size in serum due to the presence of agglomerates. The ability of TRPS to measure sample agglomeration was investigated by comparison with the high resolution technique of DCS. Particle-by-particle ζ-potential measurements by TRPS were consistent with those performed with ELS and allowed a description of the ζ-potential distribution within the samples.