Picornaviruses are +ssRNA viruses with 60 copies of each of 4 capsid proteins icosahedrally arranged around the genome. Stable capsid intermediates typically mediate picornavirus entry into host cells (e.g. Enteroviruses), but for the acid-labile foot-and-mouth disease virus (FMDV), such intermediates have remained elusive because the capsid dissociates rapidly at low pH. We used two approaches to identify these intermediates. Firstly, we used conventional cryo-EM to study the relatively acid-tolerant FMDV A1061 incubated at pH 6.2. Our 2.6 Å map shows that the N-terminus of VP1 replaced the C-terminus of VP4 in an extended β-sheet critical for capsid stability. This association of VP1 to form an extended β-sheet is structurally similar to the more acid-stable Enteroviruses, suggesting a conserved strategy for maintaining capsid integrity under acidic conditions. Secondly, we performed microsecond time-resolved cryo-EM on the highly acid-labile SAT2 serotype. SAT2 was prepared in the presence of a “caged proton” and plunge-frozen before UV-A exposure to release the protons and acidify the ice. Grids were melted in situ using a 30µs laser pulse and subsequently revitrified, thereby trapping acid-induced structural intermediates. A 3.6 Å map of the revitrified particles shows a 2% increase in diameter, along with disordering of the C-terminus of VP4, consistent with acid-induced changes in our pH 6.2-exposed A1061 strain using conventional cryo-EM. Overall, we identified two novel low-pH FMDV structures, likely intermediates in uncoating/dissociation pathways, that could shed light on FMDV entry mechanisms and aid the design of vaccines with improved stability.