The evolution of soil structure in agricultural soils is driven by natural and anthropogenic factors including inherent soil properties, climate and soil management interventions, all acting at different spatial and temporal scales. Although the causal relationships between soil structure and these individual factors are increasingly understood, their relative importance and complex interactive effects on soil structure have so far not been investigated across a geo-climatic region.Here we present the first attempt to identify the relative importance of factors that drive the evolution of soil structure in agricultural soils as well as their direction of effect with a focus on the temperate-boreal zone. This was done using a random forest (RF) approach including soil, climate, time, and site factors as covariates. Relative entropy, as quantified by the Kullback-Leibler (KL) divergence, was used as a quantitative index of soil structure, which is derived from the particle-size distribution and soil water retention data, and integrates the effects of soil structure on pores from the micrometre-scale to large macropores. Our dataset includes 431 intact topsoil and subsoil samples from 89 agricultural sites across Sweden and Norway, which were sampled between 1953 and 2017. The relative importance of covariates for the evolution of soil structure was identified and their non-linear and non-monotonic effects on the KL divergence were investigated through partial dependence analysis. To reveal any differences between topsoils (0–30 cm; n = 174) and subsoils (30–100 cm; n = 257), the same analysis was repeated separately on these two subsets.The covariates were able to explain on average more than 50% of the variation in KL divergence for all soil samples and when only subsoil samples were included. However, the predictions were poorer for topsoil samples (≈ 35%), underlining the complex dynamics of soil structure in agricultural topsoils. Parent material was the most important predictor for the KL divergence, followed by clay content for all soil samples and sampling year for only subsoil samples. Mean annual air temperature ranked third and annual precipitation ranked fourth for subsoil samples. However, it remains unclear whether the effects of climate factors are direct (e.g., freezing and thawing, wetting and drying, rainfall impact) or indirectly expressed through interactions with soil management. The partial dependence analysis revealed a soil organic carbon threshold of around 3% below which soil structure starts to deteriorate. Besides this, our results suggest that subsoil structure in the agricultural land of Sweden deteriorated steadily during the 1950′s to 1970′s, which we attribute to traffic compaction as a consequence of agricultural intensification. We discuss our findings in the light of data bias, laboratory methods and multicollinearity and conclude that the approach followed here gave valuable insights into the drivers of soil structure evolution in agricultural soils of the temperate-boreal zone. Theses insights will be of use to inform soil management interventions that address soil structure or soil properties and functions related to it.