Protoplanetary disks are dust-and gas-rich structures surrounding protostars. Depending on the distance from the protostar, this dust is thermally processed to different degrees and accreted to form bodies of varying chemical compositions. The primordial accretion processes occurring in the early protoplanetary disk such as chondrule formation and metal segregation are not well understood. One way to constrain them is to study the morphology and composition of forsteritic grains from the matrix of carbonaceous chondrites. Here, we present high-resolution ptychographic X-ray nanotomography and multimodal chemical microtomography (X-ray diffraction and X-ray fluorescence) to reveal the early history of forsteritic grains extracted from the matrix of the Murchison CM2. 5 chondrite. The 3D electron density maps revealed, at unprecedented resolution (64 nm), spherical inclusions containing Fe–Ni, very little silica-rich glass and void caps (ie, volumes where the electron density is consistent with conditions close to vacuum) trapped in forsterite. The presence of the voids along with the overall composition, petrological textures, and shrinkage calculations is consistent with the grains experiencing one or more heating events with peak temperatures close to the melting point of forsterite (∼ 2100 K), and subsequently cooled and contracted, in agreement with chondrule-forming conditions.