The early stages of soot formation, namely inception and growth, are highly debated and central to many ongoing studies in combustion research. Here, we provide new insights into these processes from studying different soot samples by atomic force microscopy (AFM). Soot has been extracted from a slightly sooting, premixed ethylene/air flame both at the onset of the nucleation process, where the particle size is of the order of 2–4 nm, and at the initial stage of particle growth, where slightly larger particles are present. Subsequently, the molecular constituents from both stages of soot formation were investigated using high-resolution AFM with CO-functionalized tips. In addition, we studied a model compound to confirm the atomic contrast and AFM-based unambiguous identification of aliphatic pentagonal rings, which were frequently observed on the periphery of the aromatic soot molecules. We show that the removal of hydrogen from such moieties could be a pathway to resonantly stabilized π-radicals, which were detected in both investigated stages of the soot formation process. Such π-radicals could be highly important in particle nucleation, as they provide a rational explanation for the binding forces among aromatic molecules.