The depletion of soil organic matter (SOM) reserve after deforestation and subsequent management practices are well documented, but the impacts of land-use change on the persistence and vulnerability of storage C and N remain uncertain. We investigated soil organic C (SOC) and N stocks in a landscape of chrono-sequence natural forest, grazing/crop lands and plantation forest in the highlands of North-West Ethiopia. We hypothesized that in addition to depleting total C and N pools, multiple conversions of natural forest significantly change the relative proportion of labile and recalcitrant C and N fractions in soils, and thus affect SOM quality. To examine this hypothesis, we estimated depletion of SOC and N stocks and labile (1 & 2) and recalcitrant (fraction 3) C and N pools in soil organic matter following the acid hydrolysis technique. Our studies showed the highest loss of C stock was in grazing land (58%) followed by cropland (50%) and eucalyptus plantation (47%), while on average ca. 57% N stock was depleted. Eucalyptus plantation exhibited potential for soil C recovery, although not for N, after 30 years. The fractionation of SOM revealed that depletions of labile 1 C stocks were similar in grazing and crop lands (36%), and loss of recalcitrant C was highest in grazing soil (56%). However, increases in relative concentrations of labile fraction 1 in grazing land and recalcitrant C and N in cropland suggest the quality of these pools might be influenced by management activities. Also, the C:N ratio of C fractions and recalcitrant indices (RIC and RIN) clearly demonstrated that land conversion from natural forest to managed systems changes the inherent quality of the fractions, which was obscured in whole soil analysis. These findings underscore the importance of considering the quality of SOM when evaluating disturbance impacts on SOC and N stocks.