Soil health and biodiversity are fundamental features for both organic production systems and of an agroecological approach. Soil health and functional biodiversity are effects of the dynamics imposed by environmental factors and crop management, and are closely related to the dynamics in soil organic matter. Within the framework of CORE Organic project ”GreenResilient”, crop rotations for “business as usual” (BAU) and innovative (INN) organic greenhouse cropping systems were designed according to local preconditions in the five countries hosting the experimental sites: Belgium (BE), Switzerland (CH), Denmark (DK), France (FR) and Italy (IT). The choice and order of crops within the various BAU and INN systems differed between countries. Soil microbial activity and biodiversity were analysed using fluorescein diacetate activity (FDA) and metagenomic analysis (Illumina MiSeq) of fungi (ITS) and bacteria (16S) at three key events, namely start, midterm and end of the two-year crop rotation. Samples were collected from three blocks (in some cases four) at a density of three replicates (resulting in 9 or 12 replicate samples per treatment). Specific disease suppressiveness was evaluated with respect to Fusarium oxysporum f.sp. lycopersici (FOL). There was no general trend with respect to microbial activity for the different cropping systems. Interestingly, the microbial activity initially rose in many of the systems (midterm) but decreased to a lower level mostly similar or insignificantly higher to the starting point. A general significant decrease in microbial activity was found at all cropping systems in IT from the start to the end of the experiment. Likewise, soil bacterial and fungal alpha diversity varied between the different sampling incidents with respect to both species richness and evenness (Chao1 index, Shannon diversity index). Interestingly, a strong shift towards richer fungal community was found for the CH-BAU systems as compared to the CH-INN systems over time (based on % change from initial sample). CH-INN systems displayed a richer bacterial community than CH-BAU systems. Similar observations were found sporadically in other systems, displaying changes in beta-diversity between systems over time. Shifts in relative abundance was found for some phyla over time within systems, but no general trend applying to all BAU or INN was registered. A presence of several types of fungal pathogens were observed in all countries, independent of production system. Microbial activity did not conclusively explain variations in microbial diversity for fungi or bacteria. No differences were found in plant performance when assessing specific suppressiveness towards FOL. As plant performance in control samples was much better than those detected in fresh soil samples, with or without amendment of FOL, the general build-up of pathogenic organisms during the crop rotations might mask direct effects