In this Part II of the paper on the evolution of carbon-rich Si–O–C polymer-derived ceramics (PDCs), emphasis is placed on the strengths and limitations of transmission electron microscopy (TEM) techniques with high lateral resolution, i.e., electron energy-loss spectroscopy (EELS), high-resolution TEM (HRTEM) and energy-filtered TEM (EFTEM). Here, the identical SiOC materials, as described in Part I. EELS studies confirmed the progression of structural rearrangements within the SiOC matrix temperatures exceeding 1200°C. High-resolution TEM imaging showed that the SiOC matrices are indeed predominantly amorphous even upon high thermal treatment. Energy-filtered TEM analysis revealed, in contrast to the results obtained by Raman spectroscopy (Part I), that the excess free carbon phase undergoes a pronounced rearrangement within the amorphous microstructure. HRTEM characterization revealed the distribution of phases within the amorphous SiOC matrix; information that is not accessible by integral spectroscopic techniques. Discrepancies between the interpretation of experimental results obtained by local versus integral characterization tools are discussed in detail.