Atomic force microscopy (AFM) cantilevers are commonly made from two material layers: a reflective coating and structural substrate. Although effective, this can result in thermally induced cantilever deflection due to ambient and local temperature changes. While this has been previously documented, key aspects of this common phenomenon have been overlooked. This work explores the impact of thermally induced cantilever deflection when in- and out-of-contact, including the topographic scan artefacts produced. Scanning thermal microscopy probes were employed to provide direct cantilever temperature measurement from Peltier and microheater sources, whilst permitting cantilever deflection to be simultaneously monitored. Optical lever-based measurements of thermal deflection in the AFM were found to vary by up to 250% depending on the reflected laser spot location on the cantilever. This highlights AFM’s inherent inability to correctly measure and account for thermal induced cantilever deflection in its feedback system. This is particularly problematic when scanning a tip in-contact with the surface, when probe behaviour is closer mechanically to that of a bridge than a cantilever regarding thermal bending. In this case, measurements of cantilever deflection and inferred surface topography contained significant artefacts and varied from negative to positive for different optical lever laser locations on the cantilevers. These topographic errors were measured to be up to 600 nm for a small temperature change of 2 K. However, all cantilevers measured showed a point of consistent, complete thermal deflection insensitivity 55% to 60% along their lengths. Positioning the reflected laser at this location, AFM scans exhibited improvements of up-to 97% in thermal topographic artefacts relative to other laser positions.