Nth-like DNA glycosylase (NTHL1) is a base excision repair enzyme, with a crucial role both in nuclear and mitochondrial genomic maintenance. In this study, we demonstrate a key function of NTHL1 on mitochondrial DNA (mtDNA) maintenance and mitochondrial dynamics. Our results reveal significant accumulation of mitochondrial transcripts and increased mtDNA levels in NTHL1-deficient cells, accompanied by an accumulation of mtDNA lesions. These findings underscore the essential role of NTHL1 in protecting against mitochondrial genomic damage. In addition to increased OXPHOS mRNA and protein levels, Seahorse analyzer measurements further demonstrated enhanced mitochondrial respiratory capacity and elevated oxygen consumption rates. Furthermore, NTHL1 deficiency was associated with increased mitochondrial size and elevated protein levels of the mitochondrial fusion protein Dynamin-like GTPase OPA1, mitochondrial, long form (L-OPA1). Notably, NTHL1 knockout cells showed resistance to 1-methyl-4-phenylpyridinium (MPP+)-induced mitochondrial stress, indicating that the loss of NTHL1 promotes mitochondrial resilience and an adaptive response to oxidative stress. Combined, these findings indicate a complex phenotype where in NTHL1 plays a multifaceted role in mitochondrial maintenance and its loss leads to mild mitochondrial dysfunction that activates mitohormesis. This study thus extends the known functions of NTHL1 beyond nuclear DNA repair, highlighting its critical role in mitochondrial health and regulation of cellular resilience to oxidative stress.