The electrochemical synthesis of ammonia through the nitrogen reduction reaction (NRR) is receiving much attention, since it is considered a promising alternative to the Haber–Bosch process. In NRR experiments, a Nafion membrane is generally adopted as a separator. However, its use is controversial since ammonia can be trapped in the membrane, to some extent, or even pass through it. We systematically investigate the interaction of a Nafion membrane with ammonia and with an electrolyte and compare it with Zirfon as a possible alternative separator. We show that Nafion containing ammonia can easily release it when immersed in a 0.1 M Na2SO4 ammonia-free electrolyte, due to the cation exchange mechanism (Na+-NH4+). Since Na2SO4 is a commonly adopted electrolyte for NRR experiments, this may cause serious measurement errors and non-reproducible results. The same experiments performed using the polysulfone Zirfon separator clearly show that it is immune to interactions with ammonia, because of its different ion conduction mechanism. The findings provide a deeper understanding of the choice of membrane and electrolyte to be adopted for NRR tests, and may allow one to obtain more accurate and reliable results.