Enzyme-linked immunosorbent assay (ELISA), the traditional antibody quantification technique, has several limitations, especially when used to evaluate multivalent and/or infant vaccines. We have developed a multiplex bead-based antibody quantification assay (MBIA) to measure antibody response to multiple pneumococcal (Pn) serotypes (St) in a single assay. MBIA was compared with the WHO ELISA using a WHO panel of 12 international calibration sera for 7 Pn Sts. An agreement of 75 to 92% was obtained for all 7 Sts. MBIA exhibited good robustness, with the assay variability at ≤ 16%. A major contributor to MBIA variability was the cell wall polysaccharide (CWPs) content in Pn St-specific capsular Ps. This necessitated careful CWPs (20 μg/ml) preadsorption of sera. MBIA is specific, robust, and reproducible and offers high throughput. The use of MBIA will greatly reduce the cost and time required to evaluate the immune response to multiple Pn Sts and could help promote the licensure of future Pn and other multivalent vaccines.