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The recent increase in foodborne disease associated with the consumption of fresh vegetables stresses the importance of the development of intervention strategies that minimize the risk of preharvest contamination. To identify risk factors for Escherichia coli O157:H7 persistence in soil, we studied the survival of a Shiga-toxin-deficient mutant in a set of 36 Dutch arable manure-amended soils (organic/conventional, sand/loam) and measured an array of biotic and abiotic manure-amended soil characteristics. The Weibull model, which is the cumulative form of the underlying distribution of individual inactivation kinetics, proved to be a suitable model for describing the decline of E. coli O157:H7. The survival curves generally showed a concave curvature, indicating changes in biological stress over time. The calculated time to reach the detection limit ttd ranged from 54 to 105 days, and the variability followed a logistic distribution. Due to large variation among soils of each management type, no differences were observed between organic and conventional soils. Although the initial decline was faster in sandy soils, no significant differences were observed in ttd between both sandy and loamy soils. With sandy, loamy and conventional soils, the variation in ttd was best explained by the level of dissolved organic carbon per unit biomass carbon DOC/biomC, with prolonged survival at increasing DOC/biomC. With organic soils, the variation in ttd was best explained by the level of dissolved organic nitrogen (positive relation) and the microbial species diversity as determined by denaturing gradient gel electrophoresis (negative relation). Survival increased with a field history of low-quality manure (artificial fertilizer and slurry) compared with high-quality manure application (farmyard manure and compost). We conclude that E. coli O157:H7 populations decline faster under more oligotrophic soil conditions, which can be achieved by the use of organic fertilizer with a relatively high C/N ratio and consequently a relatively low rate of nutrient release.