Spatiotemporal regulation of reactive oxygen species (ROS) is fine-tuned at multiple levels, including transcriptional regulation. Arabidopsis copper amine oxidase ζ (CuAOζ) is localized in peroxisomes, and the CuAOζ-derived ROS is required for indole-3-butyric acid (IBA)-induced lateral root (LR) development. Here, we showed that both GATA2 and NIGT1.2 transcription factors interacted with the 5′ untranslated region (5′ UTR) of CuAOζ, using enhanced yeast one-hybrid analysis. NIGT1.2 was highly expressed in root tips and was upregulated by IBA. Phenotypic analysis, localization, and genetic studies demonstrate that NIGT1.2 positively regulated IBA-induced CuAOζ expression, ROS generation, and LR development. Furthermore, another transcription factor, UPBEAT1 (UPB1), regulated the basal expression of CuAOζ in roots, suggesting a putative functional regulation of CuAOζ in cellular proliferation and differentiation in the root. Together, our findings indicate that transcriptional regulation of peroxisomal CuAOζ plays an important role in determining CuAOζ spatiotemporal activity and ROS homeostasis within a developing root.