Models that describe Soil Organic Carbon (SOC) dynamics ignore functional relationships that occur during land use which may confer degradation thresholds. We investigated the dynamics of soil organic matter degradation on an Oxisol following conversion of native forest vegetation to agriculture along a 100 year cultivation chronosequence in western Kenya. Seven broad categories of agricultural conversion sites were identified, representing < 3, 3-9, 10-22, 23-34, 35-57, 58-83 and > 83 years following cultivation. Soil samples were collected from randomly selected agricultural fields where maize was historically cultivated with little or no fertilizer/manure inputs. Twelve undisturbed forest reference plots were included in a paired combination with the cultivated plots. Soil samples were treated to a two step organic matter fractionation process involving density separation with sodium iodide and physical energy disruption through sonication to yield three functional organic C pools that were related to seasonal C dynamics, aggregate C protection and long-term soil C stabilization. The pools were sequentially separated from soil as light-fraction C, recovered following density flotation at 1.8 g cm^-3, aggregate-protected C, isolated after density separation following high energy sonication and organo-mineral associated C from the residue. Mass spectrometry evaluations of δ¹³C signature were used to partition resident C stocks into native forest C₃ C and contemporary C₄ crop C sources. SOC declined rapidly and reached a new equilibrium beyond 40 years of maize cultivation at which time the soil C (19 g C kg^-1) and N (2.0 g kg^-1) contents were less than 20% of the original forest C (101 g C kg^-1) and N (25.3 g kg^-1). At this new stable equilibrium point, the δ¹³ C values revealed that one half of the remaining C is of C₃ native forest origin while the other half is due to C₄ cultivated crop inputs. In addition, biogeochemical transformations of C and N within functionally specific fractions will be reported.