Soil organic matter (SOM) losses due to soil erosion may be considered low in continuous potato (Solanum tuberosum L.) cropping systems, but cumulated over time may cause considerable soil degradation. A field study was conducted in Kabete, Kenya, during the 2014 to 2015 rainy seasons to determine the effect of sediment particle size distribution on SOM losses and to assess the SOM fractions most susceptible to soil erosion under potato-legume intercropping systems. The treatments comprised of bare soil, pure potato stand (sole potato), potato + garden pea (Pisum sativa), potato + climbing bean (Phaseolus vulgaris), and potato + dolichos lablab (Lablab purpureus). A combined aggregate size and density fractionation was used to separate the sediment in size classes of aggregates 53 to 250 μm and in the sieve fraction <–53 μm, while SOM was fractionated into particulate organic matter with a density of 1.65 to 1.85 g cm−3 and mineral-associated SOM with a density of 2.60 g cm–3. Sediment and organic matter enrichments varied significantly (p < 0.05) among the cropping systems and were consistently highest under sole potato and lowest under potato + dolichos. Soil particles were transported mainly as aggregates, with those in the <53 μm size fraction containing primary silt and clay particles. Stable fractions of SOM related positively with silt plus clay particles (r = 0.89; p < 0.01) and accounted for 95% of the total SOM losses. Vegetal cover (β = –0.10508; p = 0.001603), splash detachment (β = 0.00323; p = 0.039403), and their interactive effect (β = –0.27327; p = 0.027224) influenced the amount and composition of SOM fractions at the aggregate level. Dolichos lablab ensured continuity of effective groundcover and protected the organic matter against soil erosion, thus demonstrating the need to integrate indeterminate legume cover crops into potato cropping systems.