Bovine serum albumin (BSA) adsorbed on amorphous silicon dioxide (SiO2) nanoparticles was studied as a function of pH across the range of 2 to 8. Aggregation, surface charge, surface coverage, and protein structure were investigated over this entire pH range. SiO2 nanoparticle aggregation is found to depend upon pH and differs in the presence of adsorbed BSA. For SiO2 nanoparticles truncated with hydroxyl groups, the largest aggregates were observed at pH 3, close to the isoelectric point of SiO2 nanoparticles, whereas for SiO2 nanoparticles with adsorbed BSA, the aggregate size was the greatest at pH 3.7, close to the isoelectric point of the BSA-SiO2 complex. Surface coverage of BSA was also the greatest at the isoelectric point of the BSA-SiO2 complex with a value of ca. 3 ± 1 × 1011 molecules cm−2. Furthermore, the secondary protein structure was modified when compared to the solution phase at all pH values, but the most significant differences were seen at pH 7.4 and below. It is concluded that protein–nanoparticle interactions vary with solution pH, which may have implications for nanoparticles in different biological fluids (e.g., blood, stomach, and lungs).