AbstractPhase-contrast in tapping-mode atomic force microscopy (TM-AFM) results from dynamic tip-surface interaction losses which allow soft and hard nanoscale features to be distinguished. So far, phase-contrast in TM-AFM has been interpreted using homogeneous Boltzmann-like loss distributions that ignore fluctuations. Here, we revisit the origin of phase-contrast in TM-AFM by considering the role of fluctuation-driven transitions and heterogeneous loss. At ultra-light tapping amplitudes <3 nm, a unique amplitude dependent two-stage distribution response is revealed, alluding to metastable viscous relaxations that originate from tapping-induced surface perturbations. The elastic and viscous coefficients are also quantitatively estimated from the resulting strain rate at the fixed tapping frequency. The transitional heterogeneous losses emerge as the dominant loss mechanism outweighing homogeneous losses at smaller amplitudes for a soft-material. Analogous fluctuation mediated phase-contrast is also apparent in contact resonance enhanced AFM-IR (infrared), showing promise in decoupling competing thermal loss mechanisms via radiative and non-radiative pathways. Understanding the loss pathways can provide insights on the bio-physical origins of heterogeneities in soft-bio-matter e.g., single cancer cell, tumors, and soft-tissues.