Enhancing resilience of agroecosystems of Mediterranean area is a challenge that involves both researchers and different stakeholders and, in this context, increasing crop diversity by redesigning agricultural systems can be considered among the most important tools. Therefore, the response of agroecological practices to climate change effects was tested in a long-term experiment on organic horticultural crops (MITIORG), which is characterized by a soil hydraulic arrangement in ridges, strips and the use (with different management options) of cover crops within cash crops rotations. The main objective of this study was to show how powerful is the sustainability assessment of agroecological practices by converting crops yield and biomass into energy outputs and carbon storages, in diversified horticultural systems. The obtained outputs (expressed in energy and carbon equivalents) were evaluated and analyzed considering the site-specific meteorological data in more than 10 horticultural cropping cycles, from autumn-winter 2014-15 to autumn-winter 2020-21. The Ridge and Strips (RS) system 1 (RS1 - cover crops as living mulch on ridges and break crops in strips, both with no-till termination) showed an enhancement of about 18% of energy output and carbon (C) storages compared to RS2 (ridges and strips with green manured cover) when extreme precipitation events occurred. Moreover, RS3 (ridges and strips without cover crops) recorded a reduction of about 5 and 9% of energy output and C storage, respectively, compared to the mean of RS1 and RS2 in periods with extreme events. Our results highlighted that using more diversified agroecological systems improved their overall average outputs, ensuring greater resilience during extreme weather events, since at least part of crop productions was safeguarded. Therefore, it is important to combine techniques that allow long-term resilience, such as choosing and well managing cover crops (agroecological service crops), according to site and systems specific conditions.