Zucchini (Cucurbita pepo subsp. pepo) is a seasonal vegetable (also known as courgette) characterized by health properties due to the content of several bioactive molecules. For this reason, the consumption of zucchini is highly recommended as a part of the Mediterranean diet. The aim of this study was to evaluate the possible influence of a specific compost supply for shifting the characteristics of an integrated agriculture toward a biodynamic standard following Demeter® certified rules. In particular, an approach based on 1H-Nuclear Magnetic Resonance (NMR) spectroscopy and multivariate statistical analysis (MVA) was applied to analyze the differences between the metabolic profiles of the zucchini samples (with the same cultivar, Vitulia), obtained from three different agronomical practices: two focused agricultural systems (compost supplied and integrated), as well as the used benchmark (Demeter biodynamic certified). The obtained results showed that the samples from the plots managed with biofertilizer from compost showed similar behaviour to the samples managed under Demeter biodynamic certification, with higher content of some amino acids, such as arginine, and lower content of sugars than the samples from integrated farming. The concentration of twenty elements was then determined using inductively coupled plasma atomic emission spectroscopy (ICP-AES). The averaged results of the elemental data appear almost parallel to the trend observed with the metabolomics approach. In the present case, the use of a specific compost as a biofertilizer has shown to promote the transition to the quality standards of the Demeter certification, significantly improving the crops’ sustainability.