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Compound-specific isotopic analyses were used to assess the dynamics and origin of organic matter in soils across a 30 year chronosequence where native savanna (C4) had been replaced with eucalyptus (C3). Apolar lipid fractions were recovered from plants and soils planted with Eucalyptus 0, 7.5, 17 and 30 years ago. The molecular composition of lipids in plants and soils identified three major pentacyclic triterpene methyl esters (PTMEs) specific to savanna, and three odd n-alkanes common to both vegetation types. Savanna-derived PTMEs and δ13C remained at similar levels in soils after 30 years of eucalyptus growth. 14C content of PTMEs under savanna was lower than that of bulk soil and displayed the presence of older (1,000s of years) PTMEs in soils. However, the 14C content of soil PTMEs under eucalyptus was higher than that of the soil PTMEs under savanna. This suggests both recent (10s of years) and "pre-bomb" mineralization of savanna-derived PTMEs. Compound-specific 13C analyses of soil n-alkanes showed a trend typical of a C3/C4 vegetation shift, with more depleted δ13C values with increasing time under Eucalyptus. 14C analyses of n-alkanes suggest that n-alkanes have high turnover rates in the first few years after land conversion, and n-alkane composition thereafter is dominated by eucalyptus inputs. Compound-specific analyses reveal that lipids from past vegetations remained in soils. Compound-specific analyses allow a more nuanced description of carbon turnover in soils, and may improve our mechanistic understanding of soil organic carbon dynamics.