The current project describes physical and chemical alterations that result from the thermal exposure of sunflower achenes and seeds. Specifically, achenes and seeds were heated at temperatures ranging from 130 to 600 °C under anoxic conditions for 60 min. Changes were measured in mass, relative percentages of C and N, internal and external morphology, molecular composition by direct temperature-resolved mass spectrometry (DTMS) under EI conditions, and the reflectance on polished specimens. The main constituents of sunflower seeds are lipids and protein, while the pericarps or hulls enclosing the seeds have a ligno-cellulosic structure. The morphology of achenes and seeds remains intact following exposure which makes the identification of the residues possible. The results of the sunflower experiments were compared to previous experiments conducted with peas and wheat grains. Up to approximately 340 °C, the molecular conversion of polysaccharide and protein rich peas and wheat grains follow similar pathways, while the lignin present in sunflower achenes follows its own unique pathway, resulting in a different molecular composition. At higher temperatures the molecular composition of the three propagules becomes identical. In addition the reflectance of the three propagules is identical confirming the similarity in molecular composition. Lipids show a different behaviour compared to the other three biopolymers; from 370 °C no oils are observed in the heated specimens and the DTMS-EI measurements show no lipid markers. Apart from evaporation of the triacylglycerides it is suggested that steroids have a high resistance against thermal degradation and are converted into aromatic moieties.