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Dynamic strain based atomic force microscopy (AFM) modes often fail at the interfaces where the most interesting physics occurs because of their incapability of tracking contact resonance accurately under rough topography. To overcome this difficulty, we develop a high-throughput sequential excitation AFM that captures contact dynamics of probe–sample interactions with high fidelity and efficiency, acquiring the spectrum of data on each pixel over a range of frequencies that are excited in a sequential manner. Using electrochemically active granular ceria as an example, we map both linear and quadratic electrochemical strain accurately across grain boundaries with high spatial resolution where the conventional approach fails. The enhanced electrochemical responses point to the accumulation of small polarons in the space charge region at the grain boundaries, thought to be responsible for the enhanced electronic conductivity in nanocrystalline ceria. The spectrum of data can be processed very efficiently by physics-informed principal component analysis (PCA), speeding data processing by several orders of magnitude. This approach can be applied to a variety of AFM modes for studying a wide range of materials and structures on the nanoscale.