Rhizopus rot is a common postharvest disease that causes devastating economic losses for peach producers around the world. Thus, new alternatives for the control of this disease are required. Herein we report on the obtainment of a new hydrotalcite/shilovite (HT/Sh) composite with in situ fungistatic properties on Rhizopus stolonifer. The protective effect of this composite was studied at the metabolic level by non-targeted 1H NMR metabolomics (coupled to PCA and OPLS-DA models) and RP-HPLC to determine possible changes in the primary and secondary metabolism of peaches. Our results demonstrated that the HT/Sh composite exerted a protective effect on the levels of specific sugars (glucose, ribose, and xylose) amino acids (glutamic acid, glutamine, histidine, isoleucine, leucine threonine, and valine), phenols (chlorogenic and neochlorogenic acids) and carotenoids (neoxanthin, violaxanthin, lutein, zeaxanthin, β-cryptoxanthin, and β-carotene). Our findings demonstrated that the new HT/Sh composite reported in this work was able to retard the emergence of Rhizopus rot in peaches for ten days and promoted the conservation of their nutraceutical content.