Na+/H+ antiporters are essential secondary-active transporters that are found across all biological kingdoms and play a crucial role in the pH, sodium and cell volume homeostasis. MjNhaP1 is an archaeal electroneutral Na+/H+-antiporter resembling the human NHE1 exchanger. Substrate-induced conformational changes in MjNhaP1 were examined by electron crystallography of 2D crystals in a range of physiological pH and Na+ conditions. In the absence of sodium, changes in pH had no major effect on the structure of MjNhaP1, whereas changes in Na+ concentration caused a marked conformational change that was largely pH-independent. Crystallographically determined, apparent dissociation constants indicated ~10-fold stronger Na+ binding at pH 8 than at pH 4, consistent with substrate competition for a common ion-binding site. In conjunction with a new 3D EM map of MjNhaP1 a model for transport mechanism is proposed. Conformational changes occur in the 6-helix bundle region of MjNhaP1 that is thought to harbour the ion translocation site. Na+-binding converts the antiporter from the apo- or proton-bound, outward-open state to the Na+-bound, inward-open state. Oscillation between these two states result in rapid Na+/H+ antiport.