The in situ free carbon formation in polymer-derived ceramics (PDCs) is essential for its microstructure evolution and resulting unique characteristics. This study advances the phenomenon of surface graphenization with the first silicon-based conformal preceramic polymer thin films deposited by molecular layer deposition (MLD). In situ thermal annealing transmission electron microscopy (TEM) investigation was performed to study the evolution of carbon on the nanoscale during high-temperature postprocessing of the hybrid organic−inorganic siloxane−alumina (SiAlCHO) in vacuum. The e-beam exposure during annealing induced the knock-on damage process, i.e., direct displacement/ emission of an atom as a result of the collision with a fast electron. The emission of hydrogen atoms of the preceramic MLD film led to a loss of hydrogen from the organic groups within the film, which determined the first stage of the observed phenomenon, the carbonization of the film. The relatively high annealing temperature of the sample provided the carbon mobility to form an energetically favorable sp 2 -bonding arrangement of carbon, which led to the formation of up to four graphene layers. The amount of carbon in the preceramic SiAlCHO, which is the source for the graphene layer formation, and consequently the resulting number of surficial graphene layers can be reduced by increasing the MLD process temperature so that it forms even a single layer. Micro-Raman mapping was performed to confirm the chemical nature of the e-beam-induced graphene formation. The resulting SiAlCO PDCs withstand annealing temperatures as high as 1200 °C without crystallization and phase separation. The investigation allows for a better understanding of the microstructural evolution of carbon in the near-surface region and its associated properties, which are essential for various applications of PDCs.