High throughput screening (HTS) of excipients for proteins in solution can be achieved by several analytical techniques. The screening of stabilizers for proteins adsorbed onto adjuvants, however, may be difficult due to the limited amount of techniques that can measure stability of adsorbed protein in high throughput mode. Here, we demonstrate that extrinsic fluorescence spectroscopy can be successfully applied to study the physical stability of adsorbed antigens at low concentrations in 96-well plates, using a real-time polymerase chain reaction (RT-PCR) instrument. HTS was performed on three adjuvanted pneumococcal proteins as model antigens in the presence of a standard library of stabilizers. Aluminum hydroxide appeared to decrease the stability of all three proteins at relatively high and low pH values, showing a bell-shaped curve as the pH was increased from 5 to 9 with a maximum stability at near neutral pH. Nonspecific stabilizers such as mono- and disaccharides could increase the conformational stability of the antigens. In addition, those excipients that increased the melting temperature of adsorbed antigens could improve antigenicity and chemical stability. To the best of our knowledge, this is the first report describing an HTS technology amenable for low concentration of antigens adsorbed onto aluminum-containing adjuvants.