A new tandem chromatography method was developed to directly measure the titers of various vaccine candidate molecules in cell culture without a prior purification step. The method utilized a strong anion exchange chromatography (IEC) column in tandem with a size exclusion chromatography (SEC) column to efficiently separate the nanoparticle and virus-like particle (VLP) vaccine molecules from host cell proteins and other components in the cell culture media. The dual (charge and hydrodynamic size) separation mode was deemed necessary to achieve good separation of the vaccine product for quantitation. The method development and quality assessment illustrated herein was focused on the influenza vaccine candidate H1ssF, a hemagglutinin (group 1) stabilized stem molecule fused to ferritin to form nanoparticles. This newly established method was then successfully applied to several vaccine candidate developmental projects, such as the hemagglutinin-ferritin (HAF) nanoparticle and encephalitic alphavirus VLP-based vaccines. This IEC-SEC strategy was established as a platform approach for direct titer measurement of novel vaccine molecules in cell culture.