The enzymatic controlled metabolic processes in cells occur at their optimized pH ranges, therefore cellular pH homeostasis is fundamental for life. In plants, nitrogen (N) source for uptake and assimilation, mainly in the forms of nitrate (NO3-) and ammonium (NH4+) quantitatively dominates the anion and cation equilibrium and the pH balance in cells. Here we review ionic and pH homeostasis in plant cells and regulation by N source from the rhizosphere to extra- and intra-cellular pH regulation for short and long-distance N distribution and during N assimilation. In the process of N transport across membranes for uptake and compartmentation, both proton-pumps and proton-coupled N transporters are essential, and their proton binding sites may sense change of apoplastic or intra-cellular pH. In addition, during N assimilation, carbon skeletons are required to synthesize amino acids, thus the combination of NO3- or NH4+ transport and assimilation results in different net charge and numbers of protons in plant cells. Efficient maintenance of N-controlled cellular pH homeostasis may improve N uptake and use efficiency, as well as enhance the resistance to abiotic stresses.