In greenhouses, where intensive systems are widely used for organic production, the differences between “conventionalized” and agroecological approaches are especially evident. Among the agronomic practices, green manure from agroecological service crops (ASCs) and organic amendments represent the main tools for soil fertility management with respect to the substitution of synthetic fertilizer with organic ones (the input substitution approach). Over a two-year organic rotation, we compared a conventionalized system (SB) and two agroecological systems, characterized by ASC introduction combined with the use of manure (AM) and compost (AC) amendments. A system approach was utilized for the comparison assessment. For this purpose, agronomic performance, soil fertility and the density of soil arthropod activity were monitored for the entire rotation. The comprehensive evaluation of the parameters measured provided evidence that clearly differentiated SB from AM and AC. The drivers of discrimination were soil parameters referring to long term fertility and soil arthropod dynamics. The study confirmed the higher productivity of SB but also no positive impact on soil fertility and soil arthropods, as highlighted by AM and AC. Based on the results, a trade-off between productivity and the promotion of long-term ecosystem diversity and functioning is needed for the assessment of systems of organic production.