The catalytic activity of Palladium nanoparticles synthesized via sodium bis[2-ethylhexyl] sulfosuccinate (AOT)/isooctane reverse microemulsion was studied in nitrite reduction. The influence of reaction conditions and the synthesis and purification of the nanoparticles was evaluated. In the nanoparticle size range studied (6.2–11.6 nm) a lower reaction rate and TOF were observed for small nanoparticles. This apparent structure sensitiveness results from surface blockage due to interaction of AOT with the surface of nanoparticles, as evidenced by purification with several solvents providing different removal of AOT. The activity loss was accompanied by negligible selectivity to ammonium. Large nanoparticles in buffered medium produced insignificant amount of ammonium ion for nitrite conversion values of ca. 80%. The selectivity control is ascribed to preferential blockage of the sites responsible for ammonium generation. The results show the potential of the interaction between the AOT and the nanoparticles as a tool to control catalytic selectivity.