Siliceous natural nanomaterials (SNNMs), i.e., diatomaceous earth and natural zeolites, have a nanoporous structure with large active surfaces that adsorb cations or polarized molecules. Such nanoporous feature determines the effects related to SNNM utilization as low-risk plant protectants and soil improvers. This work used SNNMs from Romanian quarries as carriers for foliar fertilizers applied to stone-fruit trees, apricot and peach. We determined the effects of SNNMs on the physiology, yield and fruit quality of the treated stone-fruit trees. SNNM application determined impacts specific to the formation of particle films on leaves: reduced leaf temperature (up to 4.5 °C) and enhanced water use efficiency (up to 30%). Foliar fertilizers’ effects on yield are amplified by their application with SNNMs. Yield is increased up to 8.1% by the utilization of SNNMs with foliar fertilizers, compared to applying foliar fertilizer alone. Diatomaceous earth and natural zeolites promote the accumulation of polyphenols in apricot and peach fruits. The combined application of SNNMs and foliar fertilizer enhance the performance of peach and apricot trees.