Root-specific and leaf-specific biomarkers have been used for decades to identify the origin of organic materials in soils and sediments. However, quantitative approaches require appropriate knowledge about the fate of these indicator molecules during degradation. To clarify this issue, we performed a 1-year incubation experiment with fine root and leaf material of six temperate tree species: European ash (Fraxinus excelsior), European beech (Fagus sylvatica), Oak spec. (Quercus spec.), Linden spec. (Tilia spec.), Norway spruce (Picea abies) and Scots pine (Pinus sylvatica). Only one molecule, x,16-dihydroxy hexadecanoic acid (x,16-C16), could be validated as a general leaf-specific biomarker for the set of all species. For roots, no general root biomarker was found. Ester-bound tricosanol (C23-OH) could be validated for five out of six species; 20-hydroxy eicosanoic acid (ωC20) could be validated for four out of six species, leaving Norway spruce without a suitable root biomarker. The results of this study suggest that the validity of leaf-and root-derived ester-bound lipids as biomarkers is highly species dependent and does not always coincide with previous findings. Concentrations of root-and leaf-derived ester-bound lipids did not stay constant within 1 year of degradation and changed without a linear trend. The change of concentrations seems to be highly species dependent. This might be due to a different structure and arrangement of the individual monomers in cutin and suberin per species, and, therefore, a different accessibility of bond cleaving enzymes. The usefulness of root and leaf biomarkers is context dependent. Our results suggest that general assumptions about litter input to forest soils solely based on biomarker analysis have to be considered carefully.