Biodiversity conservation and promotion of agroecology (including organic farming) are focused as priorities by European Commission, as reported in the Biodiversity and Farm to Fork Strategies. In this context, agricultural practices can be considered for their contribution to harnessing ecosystem services to sustain agricultural production, while minimising negative environmental effects. Among these, redesigning agricultural systems through diversification practices can be very promising by exploiting the natural biodiversity in space and time, and connecting farms with natural environments. Being an interface between above and belowground, spontaneous plants (i.e., the weeds) are considered valuable agroecosystem components that, if properly managed, provide ecosystem functions and services, and holding key role for biodiversity conservation within agroecosystems. In this study, we explored the response of spontaneous flora communities in terms of abundance, diversity, and functional traits to different soil and agrobiodiversity management strategies (soil ripping vs reduced tillage at orchard planting, soil tillage vs minimum/no tillage in orchard floor management over 5 years) and cover crop introduction in a new planted organic apricot orchard. Our results showed the strong impact of the planting operation on pre-existing spontaneous flora community structure but a resilient trajectory in the following years in recovering the previous community traits distribution. Interannual variability was the main factor affecting communities. However, the reduced tillage condition showed a conservative trend of the incidence of perennials in the community, while the introduction of cover crops generally decreased species richness and abundance. Understanding the mechanisms by which soil management practices affect weed communities can guide the designing of sustainable agroecosystems, preserving their functionality and biodiversity over time.