Maintenance of the main Golgi functions, glycosylation and sorting, is dependent on the unique Golgi pH microenvironment that is thought to be set by the balance between the rates of V-ATPase-mediated proton pumping and its leakage back to the cytoplasm via an unknown pathway. The concentration of other ions, such as chloride, potassium, calcium, magnesium, and manganese, is also important for Golgi homeostasis and dependent on the transport activity of other ion transporters present in the Golgi membranes. During the last decade, several new disorders have been identified that are caused by, or are associated with, dysregulated Golgi pH and ion homeostasis. Here, we will provide an updated overview on these disorders and the proteins involved. We will also discuss other disorders for which the molecular defects remain currently uncertain but which potentially involve proteins that regulate Golgi pH or ion homeostasis.