Calcium carbonate-based hollow or porous particles are one of the preferred carriers for fabrication of drug delivery systems. We have developed an eco-friendly method to produce calcium carbonate nanocrystals, which have shown biocompatibility and optimal capacity to across cell membrane in human cell lines providing new tools in cancer therapy. The success of drug delivery systems has paved the way for the development of systems for controlled release of agrochemicals. In this work, we exploited calcium carbonate nanocrystals as carriers for targeted release of phytodrugs investigating a potential control strategy for the pathogen Xylella fastidiosa. This pathogen is the causal agent of the Olive Quick Decline Syndrome that is an unprecedented emergency in Italy and potentially in the rest of Europe. We studied nanocrystals interactions with bacteria cells and the application in planta to verify olive plants uptake. Ultrastructural analysis by electron microscopy shown an alteration of bacteria wall following nanocrystals interaction. Nanocrystals were adsorbed from roots and they translocated in plants tissues. Calcium carbonate carriers were able to encapsulate efficiently two types of antimicrobial substances and the potential efficacy was tested in experiment under greenhouse conditions.