The bacterial acid stress-sensing chaperone HdeA loses structure to gain function. As enteropathogenic E. coli pass through the severely acidic environment of the mammalian stomach, HdeA transitions from an inactive, folded dimer to chaperone-active, unfolded monomers to protect against the acid-induced aggregation of periplasmic proteins. Toward achieving an atomic-level mechanistic understanding of the acid stress response of HdeA, we develop a multiscale modeling approach to capture its pH-dependent thermodynamics. Our approach utilizes pKa calculations from all-atom constant pH molecular dynamics simulations to alter the coarse-grained model for representing different pH environments. Changes in the thermodynamics of binding as a function of pH are explored using the efficient “Hamiltonian mapping” reweighting formalism. We propose new features of the pH-sensing mechanism of HdeA that can be directly tested by experiment. Namely, our model predicts that HdeA is maximally stable under mildly acidic conditions and that a partially unfolded dimeric intermediate may contribute to substrate binding. Our multiscale approach is general such that it can be applied toward understanding pH-dependent functional transitions in other systems and sets a foundation from which to construct models of HdeA-substrate interaction.