The incidence of Candida species resistance to traditional antifungals is increasing globally. This issue significantly impacts patients' lives and raises healthcare expenses, confirming the need for developing novel therapeutic strategies. Recently, a thermostable trypsin inhibitor was isolated from Salvia hispanica L. (chia) seeds – named ShTI (MM 11.558 kDa) with an antibacterial effect against Staphylococcus aureus species. This work aimed to assess the antifungal effect of ShTI against Candida species and its synergism with fluconazole and to evaluate its mode of action. Moreover, preliminary toxicological studies using mouse fibroblast cells were performed. ShTI displayed an anticandidal effect alone against C. parapsilosis (ATCC® 22019), C. krusei (ATCC® 6258), and six clinical fluconazole-resistant strains of C. albicans (2), C. parapsilosis (2), and C. tropicalis (2) (MIC 50: 4.1 µM and MIC 100: 8.2 µM) and exhibited a synergistic effect when combined with fluconazole against C. albicans with complete alteration of the morphological structure of the yeast. The mode of action of ShTI against C. krusei (ATCC® 6258™) and C. albicans species involves cell membrane damage due to increased membrane permeabilization, overproduction of reactive oxygen species, formation of pseudohyphae, injury of cells and pore formation and consequently cell death. In addition, ShTI (8.65 and 17.3 µM) showed a noncytotoxic and nongenotoxic effect in L929 mouse fibroblast cells. These findings make it plausible to assume that ShTI is a promising antimicrobial candidate, but new assays are required to progress the application of ShTI's potential usage as a novel antifungal.