Biological ageing is accompanied by progressive alterations in mitochondrial metabolism, microvascular function, and thermoregulation, which together shape tissue heat production and dissipation, with underlying molecular-level processes that may include quantum-scale phenomena. Passive microwave radiometry (MWR) provides a non-invasive, radiation-free detecting of deep-tissue bioenergy emissions, complementing surface infrared thermography. Here, we evaluate a thermophysiological Bioenergetic Index (BEI) derived from deep-tissue microwave emission, surface temperature, and their spatial and deep–surface relationships as a proxy for biological ageing. We analysed breast thermophysiology measurements from 36,391 women aged 20–80 years collected during routine clinical assessments. Supervised machine-learning models trained exclusively on thermal features (with chronological age used only as the target) predicted age at the individual level with MAE ≈ 3.5 years and RMSE ≈ 5.4 years (R² ≈ 0.76). Aggregation into 5-year age bins revealed a robust non-linear ageing trajectory (R² = 0.984), characterised by mid-life decline and late-life stabilisation. These findings demonstrate a strong ageing signal in female breast thermophysiology, while highlighting the need for longitudinal and cross-population validation.