Soot particles emitted from modern diesel engines, despite significantly lower total mass, show higher reactivity and toxicity than black-smoking old engines, which cause serious health and environmental issues. Soot nanostructure, i.e. the internal structure of soot particles composed of nanoscale carbon fringes, can provide useful information to the investigation of the particle reactivity and its oxidation status. This study presents the nanostructure details of soot particles sampled directly from diesel flames in a working diesel engine as well as from exhaust gases to compare the internal structure of soot particles in the high formation stage and after in-cylinder oxidation. Thermophoretic soot sampling was conducted using an in-house-designed probe with a lacy transmission electron microscope (TEM) grid stored at the tip. The soot particles deposited on the grid were imaged using a high-resolution TEM to obtain key nanostructure parameters such as carbon fringe length, tortuosity and fringe-to-fringe separation. The TEM images show that in-flame soot particles comprise multiple amorphous cores with many defective carbon fringes, which are surrounded by a more oriented and graphitised outer shell. The same core-shell structures are found in the exhaust soot particles, suggesting the overall shape developed within the diesel flame does not change during soot oxidation. However, the exhaust soot particles exhibit more oxidised and less reactive nanostructures as evidenced by the increased fringe length, reduced fringe tortuosity, and lower fringe separation distance. Three jet configurations were studied; two single-jet cases showing different jet-wall characteristics, and a double jet employing significant jet-jet interactions. The double jet configuration showed the largest differences between in-flame and exhaust soot nanostructure parameters because the soot particles formed within the fuel-rich jet-jet interaction region are more reactive.