The visible world is founded on the proton, the only composite building block of matter that is stable in nature. Consequently, understanding the formation of matter relies on explaining the dynamics and the properties of the proton's bound state. A fundamental property of the proton involves the system's response to an external electromagnetic (EM) field. It is characterized by the EM polarizabilities 1 that describe how easily the charge and magnetization distributions inside the system are distorted by the EM field. Moreover, the generalized polarizabilities 2 map out the resulting deformation of the densities in a proton subject to an EM field. They reveal essential information regarding the underlying system dynamics and provide a key for decoding the proton structure in terms of the theory of the strong interaction that binds its elementary quark and gluon constituents together. Of particular interest is a puzzle in the proton's electric generalized polarizability that remains unresolved for two decades 2 . Here we report measurements of the proton's EM generalized polarizabilities at low four-momentum transfer squared. We show evidence of an anomaly to the behaviour of the proton's electric generalized polarizability that contradicts the predictions of nuclear theory and we derive its signature in the spatial distribution of the induced polarization in the proton. The reported measurements suggest the presence of a novel, not yet understood dynamical mechanism in the proton and present significant challenges to the nuclear theory.