Candida albicans is the most predominant fungal species isolated from medical devices, including catheters, heart valves, and dental prostheses. In recent years, it has been demonstrated to be resistant to many antifungals; therefore, silver nanoparticles (AgNPs) have been proposed as an alternative. But only a handful of research is contributed to omic-based studies to study the various impacts of AgNPs on Candida species and other microorganisms. Thus, the study aims to biosynthesize AgNPs using Pelargonium-hortorum leaf and test its antifungal, cytotoxicity, and global gene expression on Candida through transcriptomic profiling. The leaf-assisted AgNPs resulted in spherical shapes with a particle size of 38 nm. The anticandidal effect demonstrated that the Minimum inhibitory concentration was 25 μg·mL−1. Later, the cytotoxicity assay reported a moderate impact on the human gingival fibroblast cells. Finally, the transcriptomic analysis demonstrated the differential gene expression of 3,871 upregulated and 3,902 downregulated genes. Thus, proving the anticandidal effect of AgNPs on Candida through RNA-seq experiments and the regulated genes is highly important to cell wall integrity, adherence, and virulence.