To establish infection in the human host, Neisseria gonorrhoeae requires access to transition metals. To prevent infection, the human body deploys nutritional immunity proteins to sequester metal ions away from the bacterial invaders. In response to infection, the host uses two metal-dependent defense mechanisms: deploying nutritional immunity proteins at the infection site and releasing free metals in the environment resulting in metal intoxication. While iron homeostasis has been previously studied, the mechanisms by which N. gonorrhoeae differentially expresses metal transport proteins or metal export proteins in response to zinc and manganese ions has been incompletely explored. Zinc and manganese are reported to be imported into the cytoplasm via a periplasmically located ABC transport system known as both ZnuCBA and MntABC. In closely related Neisseria meningitidis, a manganese exporter MntX protects the bacteria from manganese intoxication. Expression of these transport genes is thought to be regulated by the zinc uptake regulator (Zur), which is also known as PerR. In N. gonorrhoeae, literature varies on the precise mechanisms by which zinc and manganese regulate mntABC/znuCBA, potentially due to strain-to-strain variation. In this work, we investigate the Zn- and Mn- dependent responses to metal limitation and overload. We use RNA-seq, RT-qPCR, ICP-MS, growth assays, and genetic manipulation in multiple N. gonorrhoeae backgrounds to understand the differential transcriptional responses. Zinc-dependent transcriptional responses were identified in both strains FA1090 and FA19. In FA19, high levels of Mn prevented growth, suggesting Mn-intoxication. However, we were unsuccessful in identifying any Mn-dependent transcriptional responses in strain FA1090. We identified a full-length gene capable of encoding an intact MntX protein in FA1090, but the gene contains a premature stop codon in FA19 resulting in a truncated MntX. When MntXFA1090 was moved into FA19, the metal-intoxication phenotype was abrogated, suggesting MntXFA1090 can appropriately export Mn, preventing intoxication. Similarly, when mntX was knocked out in FA1090, high levels of Mn were able to prevent growth. This work shows the internal Mn pools differ between strains and that this difference can be attributed to MntX.