Bitumen is the binder in the composite material named asphalt concrete. Under cyclic mechanical loading of traffic passing over the pavement, eventually damage will initiate in the pavement, leading to eventual structural failure. This damaging process is accelerated by time dependent change of the mechanical properties of asphalt concrete due to ageing mechanisms like oxidation. Bitumen displays spatial heterogeneity at the micrometer scale, which has been observed by atomic force microscopy (AFM). The mechanical properties of the elliptical, microstructural domains of bitumen are distinct from those of the continuous phase. This introduces stiffness discontinuities in the material, which under mechanical loading will concentrate stresses at the interfaces, and thus the locations where early stages of damage will develop. This work aims at in situ probing of the crack healing of bituminous materials as a function of moderate temperature changes. The bitumen was prepared on a flexible substrate which was mechanically strained to induce damage. AFM measurements of the strained bitumen specimen provides evidence of the crack initiation at the interface and the predominant propagation of cracks through the elliptical domain phases. Healing of these cracks was observed after applying modest amounts of heat to the material. Meanwhile the process was monitored in situ with AFM. With increase of temperature one of the phases starts softening, while the material as a whole remains solid. This allows the phases to rearrange and meanwhile eliminating micro cracks at the interface.