Given their organic matter (OM) depletion, agricultural soils can act as carbon (C) sinks if adequate management practices are implemented. OM stabilisation in highly OM‐depleted agricultural soils may depend upon the allocation of OM inputs among particle size fractions that differ in their capacity to stabilise OM. In a set of vegetable garden fields, we determined the magnitude of the differences in soil C and N content between organically and conventionally managed fields and the incorporation of the increased C and N pools to the fine fractions as an indication of the stability of the soil OM accrual. It was carried out in a stockless scenario in which exogenous OM was only used in organically managed fields for the last 20 years (as opposed to conventional management only using mineral fertilisers). Organic fertilisation caused a notable increase in soil organic C and N stocks compared with mineral‐fertilised soils. Such increase remained significant below the plough depth. C and N content increased at all fractions, but the relative contribution of the fine‐silt‐plus‐clay fraction to total C and N decreased at all depths. We concluded that organic management increases soil OM storage, but overall, the stability of the increased OM stocks decreases slightly. Copyright © 2016 John Wiley & Sons, Ltd.