DddA-derived cytosine base editors (DdCBEs), that are fusions of the split-DddA halves and transcription activator-like effector (TALE) array proteins, allow focused C·G-to- T·A conversions in mitochondrial DNA1. Nevertheless, its genome-wide specificity is poorly understood. Right here we present that the mitochondrial base editor induces in depth off-target enhancing within the nuclear genome. Genome-wide, unbiased evaluation of its editome reveals lots of of off-target websites which are TALE array sequence (TAS)-dependent or -independent. TAS-dependent off-target websites within the nuclear DNA (nDNA) are sometimes specified by solely one of many two TALE repeats, difficult the precept that DdCBEs are guided by a paired TALE proteins positioned in shut proximity. TAS-independent nDNA off-target websites are incessantly shared amongst DdCBEs with distinct TALE arrays. Notably, they co-localize strongly with CTCF-binding websites and are enriched in TAD boundaries. We additionally engineered DdCBE to alleviate such off-target impact. Collectively, our outcomes have implications for the usage of DdCBEs in fundamental analysis and therapeutic functions, and counsel the necessity to completely outline and consider the off-target results of base enhancing instruments.