BackgroundKnowledge of soil aggregate formation and stability is essential, as this is important for maintaining soil functions.AimsThis study aimed to investigate the influence of organic matter (OM), the content of pedogenic iron (Fe) (oxyhydr)oxides, and aggregate size on the stability of aggregates in arable soil.MethodsTo this end, the Ap and Bt horizons of a Luvisol were sampled after 14 years of bare fallow, and the results were compared with a control field that had been permanently cropped.ResultsIn the Ap horizon, bare fallow decreased the median diameter of the 53–250 µm size fraction by 26%. Simultaneously, the mass of the 20–53 µm size fraction increased by 65%, indicating reduced stability—particularly of larger soil microaggregates—due to the lack of input of fresh OM. The range of 14carbon (14C) fraction of modern C (F14C) under bare fallow was between 0.50 and 0.90, and thus lower than the cropped site (F14C between 0.75 and 1.01), which is particularly pronounced in the smallest size fraction, indicating the presence of older C. This higher stability and the reduced C turnover in <20 µm aggregates is probably also due to having the highest content of poorly crystalline Fe (oxy)hydroxides, compared to the other size fractions, which act as a cementing agent. Colloid transport from the Ap to the Bt horizon was observed under bare fallow treatment.ConclusionsThe lack of input of OM decreased the stability of microaggregates and led to a release of mobile colloids, the transport of which can initiate elemental fluxes with as‐yet unknown environmental consequences.