The main focus when considering treatment of non-healing and infected wounds is tied to the microbial, particularly bacterial, burden within the wound bed. However, as fungal contributions in these microbial communities become more recognized, the focus needs to be broadened, and the remaining participants in the complex wound microbiome need to be addressed in the development of new treatment strategies. In this study, lecithin/chitosan nanoparticles loaded with clotrimazole were tailored to eradicate one of the most abundant fungi in the wound environment, namelyC. albicans. Moreover, this investigation was extended to the building blocks and their organization within the delivery system. In the evaluation of the novel nanoparticles, their compatibility with keratinocytes was confirmed. Furthermore, these biocompatible, biodegradable, and non-toxic carriers comprising clotrimazole (~189 nm, 24 mV) were evaluated for their antifungal activity through both disk diffusion and microdilution methods. It was found that the activity of clotrimazole was fully preserved upon its incorporation into this smart delivery system. These results indicate both that the novel carriers for clotrimazole could serve as a therapeutic alternative in the treatment of fungi-infected wounds and that the building blocks and their organization affect the performance of nanoparticles.