The functioning of societies depends on a number of goods and services provided by the natural environment. Knowledge about the benefits that humans derive from it is an important issue in the era of current environmental and climate changes. Agricultural systems and management methods (e.g. tillage, weed and pest control, fertilization, field consolidation, crop specialization and monoculture) are important for biodiversity, the presence of which is of great importance for people and the environment. The aim of this study was to assess bioenvironmental indicators such as weed flora, earthworms and terrestrial invertebrates biomass, in selected crops in an organic, integrated and conventional farming systems in southern Poland. The results showed the highest biodiversity weeds, earthworms, and terrestrial invertebrates in crops grown in the organic system in comparison to the conventional or sustainable ones, where chemical herbicides were applied. Species diversity of weeds was, on average, twice as high in the organic system (21 species) compared to the integrated and conventional systems (10–11 species). In the organic system, the highest number of weeds (average 71 pcs m–2) accompanied spring wheat and the lowest number of weeds was observed in legume-grass mixture in the first year of use (average 28 pcs m–2). The highest biomass of earthworms in the soil was estimated under winter wheat and legume-grass mixtures. This indicator was half as much in the soil under plants grown in integrated and conventional systems. Terrestrial invertebrates were also most abundant in crops grown in the organic system, indicating that this agricultural production system is conducive to maintaining high biodiversity in agroecosystems. For winter wheat cultivated in the conventional and integrated systems, the invertebrate richness index was 2.5–3 times lower than in the organic system.