Intensive agriculture has been demonstrated to be a main threat to soil biodiversity through physical and chemical disturbances of soil. Alternative systems based on lower disturbances may help to promote soil biodiversity and its role in soil functioning. However, the effects of alternative systems on soil biodiversity are still poorly understood, especially regarding soil mesofauna. In this study, we aimed to assess the effects of alternative cropping systems and practice intensity on the taxonomic and functional diversity of Collembola. Collembola were sampled for two consecutive years in 21 fields (3 plots per field) under conventional or alternative systems, namely conservation or organic systems either stable (≥7 years) or in transition (≤3 years). Indicators and indices were computed to characterize separately tillage, pesticide treatments and organic fertilization in each field. Collembola species and functional traits were investigated. Functional diversity of Collembola was assessed using species traits (i.e. traits from the literature) and by conducting length measurements directly on collected Collembola individuals (body, head, leg, antenna and furca length). Collembola diversity was highly variable between and within cropping systems and years. Species richness was notably higher in conservation than in conventional systems in the second year of the study. More specifically, low tillage and high pesticide treatment intensities increased taxonomic and functional diversity and affected species with traits adapted to the surface (i.e. scales, trichobothria). Measured Collembola body length additionally revealed the presence of larger individuals under low tillage and high pesticide treatment intensities, with similar results for other length traits. Overall, our results revealed that 1) taxonomic and functional diversity are complementary to understand the effects of agricultural practices and systems on Collembola and 2) measurement of body length is relevant to assess the effects of disturbances on the local Collembola community.