• We compared base hydrolysis and pyrolysis to trace fossil root-derived OM. • Both approaches revealed the presence of suberin monomers in calcified roots. • Pyrolysis failed to detect suberin monomers in rhizosphere and root-free sediments. • In OM-poor and fossil systems, only base hydrolysis enables tracing of root remains. Hydrolyzable lipids including suberin-derived monomers have been used to identify and quantify input of root-derived organic matter (OM) in soils. The two most common ana