Particulate matter, soot, from jet engines is relevant to environmental and health concerns. In this study, JP-8, HRJ (hydro-treated renewable jet) and FT (Fischer-Tropsch) fuels were tested in a CFM56-2C1 engine on a DC-9 aircraft. Comparisons of PM physical structure at length scales spanning aggregate to primary particle to nanostructure, all by TEM, are reported. Petroleum based JP-8 derived soot shows the nanostructure progression from amorphous to graphitic-like as a function of increasing engine power. Soots from the renewable HRJ and FT fuels exhibit significant nanostructure at each power level. Results are interpreted in terms of different soot formation regions with associated variations in temperature and local equivalence ratio. The driver for such differences is the nascent fuel composition, more specifically the different classes of components and associated pyrolytic and oxidative kinetics.