NAC (NAM, ATAF1,2, and CUC2) proteins play important roles in plant defense responses and various developmental processes. Here, we isolated NAC12 from Capsicum annuum (CaNAC12) and investigated its role in stress responses. CaNAC12 encodes a 350 amino acid protein derived from a 1053 bp cDNA, which contains five conserved motifs (A, B, C, D, and E), an N-terminal region, and a variable C-terminal region. Phylogenetic analysis showed that CaNAC12 is clustered in the phylogenetic clade of CaNAC, a specific subset of NAC transcription factors from C. annuum in China. CaNAC12 expression was strongly induced by infection with Xanthomonas axonopodis pv. glycines 8ra, as well as by salicylic acid, abscisic acid, and in red fruits of chili pepper plants. CaNAC12-overexpressing plants showed significantly increased resistance to salt, drought, and Botrytis cinerea infection. Under salt stress conditions, the transgenic lines exhibited higher chlorophyll content, better shoot and root growth, and increased lateral root formation compared to control plants. Under water scarcity, the leaves of the control plants wilted severely compared to those of the transgenic lines, suggesting that CaNAC12 plays a positive role in drought tolerance. RT-PCR analysis also showed higher expression of NbDHN1, NbLEA, and NbHSR203 in the transgenic lines compared to the control plants. In addition, CaNAC12 overexpression improved resistance to Botrytis cinerea infection, as evidenced by a decreased disease index and smaller lesion size compared to the control group. Overall, our results indicate that CaNAC12 is a potential candidate gene involved in both abiotic and biotic tolerance mechanisms.