BACKGROUNDGrowing concerns about sustainability have driven the search for eco‐friendly pest management solutions. Combining natural and synthetic compounds within controlled release systems is a promising strategy. This study investigated the co‐encapsulation of the natural compound citral (Cit) and the synthetic antifungal cyproconazole (CPZ) using two water‐based nanocarriers: solid lipid nanoparticles (SLNs) and chitosan nanoparticles (CSNPs).RESULTSBoth CSNPs and SLNs loaded with Cit + CPZ displayed superior antifungal activity against Botrytis cinerea compared to free compounds. Notably, CSNPs with a 2:1 Cit:CPZ ratio exhibited the highest efficacy, achieving a minimum inhibitory concentration (MIC100) of < 1.56 μg mL−1, lower than the 12.5 μg mL−1 of non‐encapsulated compounds. This formulation significantly reduced the required synthetic CPZ while maintaining efficacy, highlighting its potential for environmentally friendly pest control.CONCLUSIONThe successful co‐encapsulation of Cit + CPZ within CSNPs, particularly at a 2:1 ratio, demonstrates a promising approach for developing effective and sustainable antifungal formulations against B. cinerea. © 2024 Society of Chemical Industry.