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Sustainable agricultural practices are increasingly becoming a strategic asset for global and national environmental policies and economy. A big challenge is the selection of appropriate indicators to describe the complexity of the agroecosystem management. In the present work, the sustainability of grape production, in vineyard trials of Pinot blanc and Rhine Riesling, managed with integrated (INT) and organic management (organic, with cattle manure ORG1 and organic with green manure ORG2), was compared using a multi-indicator approach. The experiment was set in 2011 (1.5 ha in Trento, Italy) and carbon footprint (CF), nitrogen footprint (NF), water footprint (WF), soil microbial diversity (alpha diversity of bacteria, fungi, oomycetes communities) and soil C stock change, were evaluated in 2018. The CF was 0.213—0.227 kg CO2-eq/kg in the INT, 0.144—0.168 kg CO2-eq/kg in ORG1 and 0.134—0.147 kg CO2-eq/kg in ORG2. The NF was around 1 g Nr/kg for the INT, 0.4 g Nr/kg for ORG1 and 0.5 g Nr/kg for ORG2. The WF, excluding the pesticides impact on grey water, was 666—708 L/kg for INT, 605—655 L/kg for ORG1 and 529—580 L/kg for ORG2. The impact of farming practices on soil microbial alpha diversity showed no significant difference among treatments for oomycetes and significantly higher indexes for fungi and bacteria in the ORG1, with INT and ORG2, being similar. No difference in bulk organic C were observed among treatments. Overall, the multi-indicator approach allowed to demonstrate that the organic management was more beneficial for most of the environmental spheres of the agroecosystem compared to integrated management, without affecting the grape yield.