Fascination using green synthesis methods is growing rapidly, attracting researchers to seek safer and more biocompatible processes for nanoparticle production. This study introduces a pioneering approach to crafting and investigating the antifungal effect of environmentally friendly carbon dots (organic materials) prepared from neem, rosemary, magnesium oxide (MgO), and zinc oxide (ZnO) nanoparticles (inorganic materials). MgO nanoparticles were synthesized using a Salvia hispanica (chia seed) extract. In contrast, ZnO nanoparticles were prepared from zinc acetate dihydrate and an aqueous extract of Dahlia pinnata leaves. Stable carbon nanodots were prepared from Azadirachta Indica leaves (commonly known as neem leaves) and Rosmarinus officinalis L. leaves (commonly known as rosemary leaves). This research delves into the intricate mechanisms governing their efficacy, offering insights into their potential therapeutic applications against microbial illnesses. The study illuminates their structural and functional attributes by employing various characterization methods, including FTIR, SEM, DLS, XRD, UV-vis-nir, and zeta potential. Moreover, it underscores the versatility of these materials in biomedical and environmental realms, highlighting their potential for various applications. Using the crystal violet bioassay method, we evaluated their antifungal potential against Candida albicans biofilm production. This study reveals the significant antifungal properties of these nanomaterials, hinting at their potential in combating fungal infections and advancing the fight against microbial threats. We collected three Candida albicans isolates recovered from clinical samples and examined the antifungal effect of carbon nanodots, MgO, and ZnO NPs by varying their concentrations. We coated the microtiter plate with 2,5-dimercapto-1,3,4-thiadiazole (DMcT) and then coated it with the nanodots. We observed a significant efficacy at higher concentrations. Our study unveils this unexplored area, which has been quite mysterious and more or less not understood scientifically, particularly at the molecular scale. However, it has been a traditional practice for many centuries in certain parts of the world, especially in India, where extracts prepared using plant parts, such as leaves, roots, stems, and flowers, have been used for healing and recovery from certain diseases, such as chicken pox and smallpox.