The potential of agricultural soils to sequester soil organic carbon (SOC) is affected by changes in the capacity of the mineral matrix to hold and protect SOC that are brought about by agriculture. It is well established that microaggregates provide much of the capacity of soils to protect SOC. In this study, a loss of the capacity of soils to sequester SOC following agriculture was established by comparing samples of an Alfisol, in (1) its virgin condition, (2) following relatively light treatments for agriculture, (3) following conventional cultivation for ∼120 years, and (4) after 18 years under zero tillage following ∼100 years under conventional cultivation. It appears that material has been lost from clay and silt fractions relative to sand-size material. Microaggregates in all of the cultivated soils studied were less stable to the ‘chemical hammer’ of osmotic pressure than those in the virgin soil. The introduction of no-till methods did not restore the stability of microaggregates over a period of 18 years following ∼100 years of conventional cultivation. Pore size distributions from mercury intrusion showed that cultivation always led to a decrease of pore volume in the range of pores between 0.03 and 100 μm.