The aim of the present study was to determine the short-term effects (three years) of four sustainable management systems including different carbon inputs (compost, pruning residues and cover crops, applied solely or combined) on the mineral content of soil, olive trees and weeds, on some specific groups of soil microorganisms, and on weed mycorrhizal colonization in an olive orchard compared to a conventional system involving soil tillage and only mineral forms of fertilizers. The study was performed between 2013 and 2015 in a 40-year-old olive plantation. The results showed that soil organic matter, as well as main macro- and micronutrients, were markedly improved following three years of increased biomass inputs. Data related to the mycorrhizal colonization of spontaneous weed flora and to actinobacteria, Azotobacter and proteolytic bacteria suggest favourable effects on soil biology and agro-ecosystem complexity. Sowing a mixture of winter cover crops for three successive years also contributed to soil enrichment in biological as well as mineral nutrient aspects. Adoption of the sustainable management here applied practices is in complete agreement with the European policy on the transition from a linear to a circular economy and would provide significant benefits for rural stakeholders and ecosystems in the long term.