Stable microaggregates can physically protect occluded soil organic matter (SOM) against decomposition. We studied the effects of agricultural management on the amount and characteristics of microaggregates and on SOM distribution in a marine loam soil in the Netherlands. Three long-term farming systems were compared: a permanent pasture, a conventional-arable system and an organic-arable system. Whole soil samples were separated into microaggregates (53–250 µm), 20–53 µm and <20 µm organo-mineral fractions, sand and particulate organic matter, after complete disruption of macroaggregates. Equal amounts of microaggregates were isolated, irrespective of management. However, microaggregates from the pasture contained a larger fraction of total soil organic C and were more stable than microaggregates from the two arable fields, suggesting greater SOM stabilization in microaggregates under pasture. Moreover, differences in the relative contribution of coarse silt (> 20 µm) versus fine mineral particles in the microaggregates of the different management systems demonstrate that different types of microaggregates were isolated. These results, in combination with micromorphological study of thin sections, indicate that the great earthworm activity under permanent pasture is an important factor explaining the presence of very stable microaggregates that are relatively enriched in organic C and fine mineral particles. Despite a distinctly greater total SOM content and earthworm activity in the organic- versus the conventional-arable system, differences in microaggregate characteristics between both arable systems were small. The formation of stable and strongly organic C-enriched microaggregates seems much less effective under arable conditions than under pasture. This might be related to differences in earthworm species' composition, SOM characteristics and/or mechanical disturbance between pasture and arable land.