Surface temperature measurement of lithium-ion cells provides a limited view of internal physical processes during charging. Using a recently developed non-invasive battery internal temperature sensor, we now demonstrate that anode temperature reflects physically-based dynamics at the anode that were previously obscured by cell-surface measurements. First, using automated segmentation with a maximum-likelihood piecewise-linear statistical model, we show that features in the anode temperature reproducibly coincide with phase transitions into Stages IVd, IV and I of graphitic carbon lithiation at various charging rates. Second, we show that anode temperature peaks around 61% state of charge, intermediate between Stages II and I of the lithiated graphitic carbon. Third, we demonstrate a sharp and sustained increase in anode temperature at variable state of charge above 85%. These findings open the possibility for improved state-of-charge estimation and adaptive charging profiles that safely reduce charging time.